## ----setup, include=FALSE, results='asis', warning=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, tidy = TRUE, warning = FALSE, message = FALSE) options(width = 800) ## ----InstallPackage, eval=FALSE, message=FALSE, warning=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("TimiRGeN") ## ----Loadlibs(TimiRGeN Mm), echo=TRUE, message=FALSE, results='hide'---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- library(TimiRGeN) library(org.Mm.eg.db) ## ----Load knitr kableExtra, echo=FALSE, warning=FALSE, error=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(knitr) library(kableExtra) ## ----Load mm data------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("mm_miR") data("mm_mRNA") ## ----Start MAE, message=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE <- startObject(mm_miR, mm_mRNA) ## ----retrieveID data for mm data, warning=FALSE, message=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE <- getIdsMir(MAE = MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, miRPrefix = 'mmu') MAE <- getIdsMrna(MAE = MAE, assay(MAE, 2), mirror = 'useast', species = 'mmusculus', orgDB = org.Mm.eg.db) ## ----combineGenes + filter, error=FALSE, warning=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ MAE <- combineGenes(MAE = MAE, miR_data = assay(MAE, 1), assay(MAE, 2)) MAE <- genesList(MAE = MAE, method = 'c', genetic_data = assay(MAE, 9), timeString = "D") MAE <- significantVals(MAE = MAE, method = 'c', geneList =metadata(MAE)[[1]], maxVal = 0.05, stringVal = "adjPVal") ## ----add entrezIDs and extract, warning=FALSE, error=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE <- addIds(MAE = MAE, method = 'c', filtered_genelist = metadata(MAE)[[2]], miR_IDs = assay(MAE, 3), mRNA_IDs = assay(MAE, 7)) MAE <- eNames(MAE = MAE, method = 'c', gene_IDs = metadata(MAE)[[3]]) ## ----downloadGTM show, message=FALSE, warning=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- MultiAssayExperiment() # # MAE2 <- dloadGmt(MAE = MAE2, species = "Mus musculus") ## ----downloadGTM working, message=FALSE, warning=FALSE, echo=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # dloadGmt failed on bioconductor vignette build so mm_gmt is added instead load(file = "../inst/extdata/mm_gmt.rda") MAE2 <- mm_gmt ## ----enrichwiki, warning=FALSE, message=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- enrichWiki(MAE = MAE2, method = 'c', # ID_list = metadata(MAE)[[4]], # orgDB = org.Mm.eg.db, # path_gene = assay(MAE2, 1), # path_name = assay(MAE2, 2), # ID = "ENTREZID", # universe = assay(MAE2, 1)[[2]]) ## ----Quickbar, warning=FALSE, message=FALSE, eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # savePlots(largeList = metadata(MAE2)[[1]], # maxInt = 5, # fileType = "jpeg") ## ----echo=FALSE, out.width = " 350px",out.height= "300px", dpi=8-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("D1_wikipathways.png") knitr::include_graphics("D2_wikipathways.png") ## ----echo=FALSE, out.width = "350px", out.height="300px", dpi=8--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("D3_wikipathways.png") knitr::include_graphics("D7_wikipathways.png") ## ----echo=FALSE, out.width = "350px", out.height="300px", dpi=8--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("D14_wikipathways.png") ## ----wikilist show, eval=FALSE, message=FALSE, warning=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # MAE2 <- wikiList(MAE2, stringSpecies = 'Mus musculus', stringSymbol = 'L') ## ----wikilist working, echo=FALSE, message=FALSE, warning=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # wikiList takes a large amount of time to complete, so to speed vignette # building, w_list_mouse is used. metadata(MAE2)[["wp_list"]] <- w_list_mouse ## ----wikiMatrix_Real, message=FALSE, warning=FALSE, echo=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE2 <- wikiMatrix(MAE = MAE2, ID_list = metadata(MAE)[[4]], wp_list = metadata(MAE2)[[1]]) ## ----wikiMatrix_Show, message=FALSE, warning=FALSE, eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- wikiMatrix(MAE = MAE2, ID_list = metadata(MAE)[[4]], # wp_list = metadata(MAE2)[[2]]) ## ----Percent, message=FALSE, warning=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ MAE2 <- turnPercent(MAE = MAE2, wikiMatrix = assay(MAE2, 4)) ## ----createClusters_slow, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # MAE2 <- createClusters(MAE = MAE2, method = "c", # percentMatrix = assay(MAE2, 5), # noClusters = 4, variance = 0.99) ## ----createClusters working, fig.align ="center",dpi=80, echo=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # The createClusters function downloads data from the internet so it cannot # pass bioconductor vignette building. For this reason clusterdata, mfuzzdata # and clusters is imported from extdata. load("../inst/extdata/clusterdata.rda") load("../inst/extdata/mfuzzdata.rda") MAEx <- MultiAssayExperiment(list('ClusterData' = clusterdata, 'MuzzData' = mfuzzdata)) MAE2 <- c(MAE2, MAEx) load("../inst/extdata/clusters.rda") metadata(MAE2)[['Clusters']] <- clusters ## ----clusterCheck, message=FALSE, warning=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # clusterCheck(Clusters = metadata(MAE2)[[3]], W = FALSE) ## ----plot fuzzy clusters, message=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # quickFuzz(Mfuzzdata = experiments(MAE2)[[7]], Clusters = metadata(MAE2)[[3]], # W = FALSE, background = "white", subcol = "black", # labelcol = "black", axiscol = "black", axisline = "black") ## ----FUZZ, echo=FALSE, out.width="800px", out.height="300px", dpi=8----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("Fuzz.jpeg") ## ----retrun cluster 1, warning=FALSE, message=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE2 <- returnCluster(MAE2, clusterData = assay(MAE2, 6), whichCluster = 1, fitCluster = 0.4) ## ----diffExpressRes, warning=FALSE, message=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE2 <- diffExpressRes(MAE = MAE2, df = assay(MAE, 1), dataType = "Log2FC", genes_ID = assay(MAE, 3), name = "miR_log2fc") MAE2 <- diffExpressRes(MAE = MAE2, df = assay(MAE, 2), dataType = "Log2FC", genes_ID = assay(MAE, 7), name = "mRNA_log2fc") ## ----mRNAs of interest, warning=FALSE, message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE2 <- reduceWiki(MAE = MAE2, path_data = assay(MAE2, 3), stringWiki = 'Lung fibrosis') MAE2 <- wikiMrna(MAE2, mRNA_express = assay(MAE2, 10), singleWiki = assay(MAE2, 11), stringWiki = 'Lung fibrosis') ## ----Correlation matrix, warning=FALSE, message=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE3 <- MultiAssayExperiment() MAE3 <- mirMrnaInt(MAE = MAE3, miR_express = assay(MAE2, 9), GenesofInterest = assay(MAE2, 12), maxInt = 5) ## ----miR-mRNA interaction databases, message=FALSE, warning=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # options(timeout=80) # MAE3 <- dloadTargetscan(MAE = MAE3, species="mmu") # # MAE3 <- dloadMirdb(MAE = MAE3, species="mmu", orgDB = org.Mm.eg.db) # # MAE3 <- dloadMirtarbase(MAE = MAE3, species="mmu") ## ----Data mining show, message=FALSE, warning=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE3 <- dataMiningMatrix(MAE = MAE3, corrTable = assay(MAE3, 1), # targetscan = assay(MAE3, 2), # mirdb = assay(MAE3, 3), # mirtarbase = assay(MAE3, 4)) ## ----Datamining working, echo=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Because the dload functions could not be performed in vignette building, # Int_data is included. load("../inst/extdata/Int_data.rda") X <- MultiAssayExperiment(list(MiningMatrix = Int_data)) MAE3 <- c(MAE3, X) ## ----matrixFilter show, warning=FALSE, message=FALSE, eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE3 <- matrixFilter(MAE = MAE3, miningMatrix = assay(MAE3, 5), # negativeOnly = TRUE, # predictedOnly = FALSE, # threshold = 2, # maxCor = -0.5) ## ----matrixFilter working, warning=FALSE, message=FALSE, echo=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Because dload functions are not evaluated, assay(MAE3, 5) should be # assay(MAE3, 2). MAE3 <- matrixFilter(MAE = MAE3, miningMatrix = assay(MAE3, 2), negativeOnly = TRUE, predictedOnly = FALSE, threshold = 2, maxCor = -0.5) ## ----CreateNetwork, message=FALSE, warning=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # MAE3 <- makeNet(MAE = MAE3, filt_df = assay(MAE3, 6)) # # quickNet(net = metadata(MAE3)[[1]]) ## ----netmake, echo=FALSE, dpi=8----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("NetPlot.jpeg") ## ----Hierarchical1, message=FALSE, warning=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # quickPathwayTC(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10), morethan = TRUE, threshold = 1, # pathwayname = "Lung fibrosis") # # quickDendro(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10), pathwayname = "Lung fibrosis") # # quickDMap(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), mRNA_exp = assay(MAE2, 10), pathwayname = "Lung fibrosis") # # quickHClust(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10), pathwayname = "Lung fibrosis", k = 3, # cluster = 1) # ## ----qpTC, echo=FALSE, out.width = "400px",out.height= "400px", dpi=8--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("pathplot.png") knitr::include_graphics("dendro.jpeg") ## ----corranalysis, message=FALSE, warning=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # quickMap(filt_df = assay(MAE3, 6), numpairs = 11) # # quickTC(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10), pair = 1, scale = FALSE, # Interpolation = TRUE, timecourse = 14) # # quickCrossCorr(filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10), pair = 1, scale = FALSE, # Interpolation = FALSE) ## ----corplot, echo=FALSE, out.width = "400px",out.height= "400px", di = 8----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("corplot.png") knitr::include_graphics("ccplot.png") ## ----reganaysis, message=FALSE, warning=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE3 <- multiReg(MAE = MAE3, gene_interest = "Igf1", mRNAreg = TRUE, # filt_df = assay(MAE3, 6), miRNA_exp = assay(MAE2, 9), # mRNA_exp = assay(MAE2, 10)) # # # model1 <- linearRegr(mreg = assay(MAE3, 7), colpair = 3, alterpairs = c(4, 5)) # summary(model1$regression) # # model2 <- linearRegr(mreg = assay(MAE3, 7), colpair = 5) # summary(model2$regression) # # quickTCPred(model = model1, reg_df = assay(MAE3, 7)) # # quickReg(reg_df = assay(MAE3, 7), colselect = 3) # quickReg(reg_df = assay(MAE3, 7), colselect = 6) ## ----TCpred, ig.align="center", echo=FALSE, out.width = "500px",out.height= "500px", di = 8----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("predred.png") ## ----Make Output for Pathvisio show, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE3 <- makeMapp(MAE3, # filt_df = assay(MAE3, 6), # miR_IDs_adj = assay(MAE, 5), # dataType = 'L') # # MAE3 <- makeDynamic(MAE = MAE3, # miR_expression = assay(MAE2, 9), # mRNA_expression = assay(MAE2, 10), # miR_IDs_adj = assay(MAE, 5), # dataType = 'L') # # write.table(assay(MAE3, 8), "MAPP.txt", quote = FALSE, # row.names = FALSE, col.names = FALSE, # sep = "\t") # # write.csv(assay(MAE3, 9), "Dynamics.csv", row.names = TRUE, # quote = FALSE) ## ----cytoscape, message=FALSE, warning=FALSE, eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # RCy3 :: cytoscapePing() # # cytoMake(assay(MAE3, 6), # titleString = 'Lung Fibrosis Pathway', # collectionString = 'PathwaysforKidneyFibrosis') ## ----loadhuman, message=FALSE, warning=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- library(org.Hs.eg.db) data("hs_miR") rownames(hs_miR) <- gsub(rownames(hs_miR), pattern = "\\.", replacement = "-") rownames(hs_miR) <- sub("-$", "*", rownames(hs_miR)) ## ----loadmRNA, message=FALSE, warning=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("hs_mRNA") MAE <- startObject(hs_miR, hs_mRNA) MAE <- getIdsMir(MAE = MAE, assay(MAE, 1), orgDB = org.Hs.eg.db, miRPrefix = 'hsa') MAE <- getIdsMrna(MAE = MAE, assay(MAE, 2), mirror = 'useast', species = 'hsapiens', orgDB = org.Hs.eg.db) ## ----addPrefix, message=FALSE, warning=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 1), prefixString = "miR") MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 2), prefixString = "mRNA") ## ----siggenes, warning=FALSE, message=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MAE <- genesList(MAE = MAE, method = 's', miR_data = assay(MAE, 9), mRNA_data = assay(MAE, 10)) MAE <- significantVals(MAE = MAE, method = 's', geneList = metadata(MAE)[[1]], maxVal = 0.05, stringVal = "adjPVal") ## ----getensemblids, warning=FALSE, message=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ MAE <- addIds(MAE = MAE, method = 's', filtered_genelist = metadata(MAE)[[2]], miR_IDs = assay(MAE, 4), mRNA_IDs = assay(MAE, 8)) MAE <- eNames(MAE = MAE, method = 's', gene_ID = metadata(MAE)[[3]]) ## ----hs dloadGmt show, eval=FALSE, message=FALSE, warning=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- MultiAssayExperiment() # # MAE2 <- dloadGmt(MAE = MAE2, species = "Homo sapiens") ## ----convert to ensembl, eval=FALSE, message=FALSE, warning=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- gmtEnsembl(MAE = MAE2, path_gene = assay(MAE2, 1), # path_data = assay(MAE2, 3), # orgDB = org.Hs.eg.db) ## ----hs dloadGmt working, echo=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # dloadGmt failed on bioconductor vignette build so hs_gmt is added instead # hs_gmt contains the MAE that would have been produced by gmtEnsembl. load(file = "../inst/extdata/hs_gmt.rda") MAE2 <- hs_gmt ## ----message=FALSE, warning=FALSE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("hs_probes") # # MAE2 <- enrichWiki(MAE = MAE2, method = 's', # ID_list = metadata(MAE)[[4]], # orgDB = org.Hs.eg.db, # path_gene = assay(MAE2, 4), # path_name = assay(MAE2, 2), # ID = 'ENSEMBL', # universe = hs_probes$ensembl_gene_id) # ## ----saveplots_s, eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # savePlots(largeList = metadata(MAE2)[[1]], maxInt = 6, # fileType = "jpeg") ## ----human wikiList show, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # MAE2 <- wikiList(MAE = MAE2, stringSpecies = "Homo sapiens", # stringSymbol = "En") ## ----human wikiList working, echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Loading w_list_human instead to speed up vignette building load("../inst/extdata/w_list_human.rda") metadata(MAE2)[['wikilist']] <- w_list_human ## ----create_percent_matrix, warning=FALSE, message=FALSE, eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- wikiMatrix(MAE = MAE2, ID_list = metadata(MAE)[[4]], # wp_list = metadata(MAE2)[[2]]) # # MAE2 <- turnPercent(MAE = MAE2, wikiMatrix = assay(MAE2, 6)) ## ----ensembl human clusters show, warning=FALSE, message=FALSE, eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # MAE2 <- createClusters(MAE = MAE2, method = "s", # dataString = "mRNA", # percentMatrix = assay(MAE2, 7), # noClusters = 2, # variance = 0.99) # # clusterCheck(Clusters = metadata(MAE2)[[3]], W = FALSE) # # quickFuzz(Mfuzzdata = experiments(MAE2)[[9]], # Clusters = metadata(MAE2)[[3]], # W = FALSE) # # MAE2 <- returnCluster(MAE2, clusterData = assay(MAE2, 8), # whichCluster = 1, # fitCluster = 0.5) # ## ----mRNA only, message=FALSE, warning=FALSE, eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("mm_mRNA") # # Data <- startObject(miR = NULL, mRNA = mm_mRNA) # # Data <- getIdsMrna(MAE = Data, mRNA = assay(Data, 2), mirror = 'useast', species = 'mmusculus', orgDB = org.Mm.eg.db) # # Data <- genesList(Data, # method = 'c', # genetic_data = assay(Data, 2), # timeString = 'D') # # Data <- significantVals(Data, method = 'c', # geneList = metadata(Data)[[1]], # maxVal = 0.05, # stringVal = 'adjPVal') # # Data <- addIds(MAE = Data, method = 'c', # filtered_genelist = metadata(Data)[[2]], # miR_IDs = assay(Data, 3), # mRNA_IDs = assay(Data, 3)) # # Data <- eNames(MAE = Data, method = 'c', # gene_IDs = metadata(Data)[[3]]) # # Data2 <- MultiAssayExperiment() # # Data2 <- dloadGmt(MAE = Data2, species = "Mus musculus") # # Data2 <- enrichWiki(MAE = Data2, method = 'c', # ID_list = metadata(Data)[[4]], # orgDB = org.Mm.eg.db, # path_gene = assay(Data2, 1), # path_name = assay(Data2, 2), # ID = "ENTREZID", # universe = assay(Data2, 1)[[2]]) # # quickBar(X = metadata(Data2)[[1]][[1]], Y = names(metadata(Data2)[[1]][1])) ## ----Long_analysis, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # library(TimiRGeN) # library(org.Hs.eg.db) # # data(long_data) # miRNA <- long_data[c(1:105),] # mRNA <- long_data[-c(1:105),] # # MAE <- startObject(miRNA, mRNA) # # MAE <- getIdsMir(MAE = MAE, miR = MAE[[1]], orgDB = org.Hs.eg.db, # miRPrefix = "hsa") # # MAE <- getIdsMrna(MAE = MAE, mRNA = MAE[[2]], mirror = "www", # species = "hsapiens", orgDB = org.Hs.eg.db) # # MAE <- combineGenes(MAE = MAE, miR_data = MAE[[1]], mRNA_data = MAE[[2]]) # # MAE <- genesList(MAE = MAE, method = "c", genetic_data = MAE[[9]], # timeString = "H", miR_data = ) # # MAE <- addIds(MAE = MAE, method = "c", filtered_genelist = metadata(MAE)[[1]], # miR_IDs = MAE[[3]], mRNA_IDs = MAE[[7]]) # # MAE <- eNames(MAE = MAE, method = "c", gene_IDs = metadata(MAE)[[2]]) # # MAE2 <- MultiAssayExperiment() # # MAE2 <- dloadGmt(MAE = MAE2, species = "Homo sapiens") # # MAE2 <- enrichWiki(MAE = MAE2, method = "c", ID_list = metadata(MAE)[[3]], # orgDB = org.Hs.eg.db, path_gene = MAE2[[1]], # path_name = MAE2[[2]], ID = "ENTREZID", # universe = MAE2[[1]][[2]]) # # quickBar(metadata(MAE2)[[1]][[1]], Y = "Enriched Pathways") # ## ----longclutsers, warning=FALSE, message=FALSE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # library(TimiRGeN) # library(org.Hs.eg.db) # # data(long_data) # miRNA <- long_data[c(1:105),] # mRNA <- long_data[-c(1:105),] # # MAE <- startObject(miRNA, mRNA) # # MAE <- getIdsMir(MAE = MAE, miR = MAE[[1]], orgDB = org.Hs.eg.db, # miRPrefix = "hsa") # # MAE <- getIdsMrna(MAE = MAE, mRNA = MAE[[2]], mirror = "www", # species = "hsapiens", orgDB = org.Hs.eg.db) # # MAE <- combineGenes(MAE = MAE, miR_data = MAE[[1]], mRNA_data = MAE[[2]]) # # MAE <- createClusters2(MAE = MAE, genetic_data = assay(MAE, 9)) # # quickFuzz(Mfuzzdata = MAE[[11]], Clusters = metadata(MAE)[[1]], # ylab="Standardised Gene Expression") # # MAE <- clusterList(MAE = MAE, clusterData = assay(MAE, 10), # fitCluster = 0.5, miR_IDs = assay(MAE, 3), # mRNA_IDs = assay(MAE, 7)) # # MAE2 <- MultiAssayExperiment() # # MAE2 <- dloadGmt(MAE = MAE2, species = "Homo sapiens") # # MAE2 <- enrichWiki(MAE = MAE2, method = "c", ID_list = metadata(MAE)[[2]], # orgDB = org.Hs.eg.db, path_gene = MAE2[[1]], # path_name = MAE2[[2]], ID = "ENTREZID", # universe = MAE2[[1]][[2]]) # # savePlots(largeList = metadata(MAE2)[[1]], maxInt = 5, fileType = "png") ## ----loadUUO, message=FALSE, warning=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ data("UUO_data") UUO_miRNA <- UUO_data[c(1:240),] UUO_mRNA <- UUO_data[-c(1:240),] ## ----netcontrast,out.width="400px",out.height="400px",echo=FALSE,dpi=8-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("NetPlot.jpeg") knitr::include_graphics("net2.jpeg") ## ----regcontrast,out.width="400px",out.height="400px",echo=FALSE,dpi=8-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::include_graphics("reg1.png") knitr::include_graphics("reg2.png")