## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set( concordance=TRUE ) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("epihet") ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("TheJacksonLaboratory/epihet") ## ----eval=FALSE,message=FALSE------------------------------------------------- # library(epihet) ## ----echo=FALSE--------------------------------------------------------------- options(continue = ' ') ## ----------------------------------------------------------------------------- files = c(system.file("extdata","D-2238.chr22.region.methClone_out.gz",package = "epihet"), system.file("extdata","D-2668.chr22.region.methClone_out.gz",package = "epihet"), system.file("extdata","N-1.chr22.region.methClone_out.gz",package = "epihet"), system.file("extdata","N-2.chr22.region.methClone_out.gz",package = "epihet")) ids = epihet::splitn(basename(files),"[.]",1) ## ----------------------------------------------------------------------------- GR.List = epihet::makeGR(files = files, ids = ids, cores = 1, sve = FALSE) ## ----results='hide'----------------------------------------------------------- comp.Matrix = epihet::compMatrix(epi.gr = GR.List, outprefix = NULL, readNumber = 60, p = 1, cores = 1, sve = FALSE) ## ----eval=FALSE--------------------------------------------------------------- # data(myValues,package = "epihet") # myGR.List<-list() # for (n in names(GR.List)) { # tmp<-GR.List[[n]] # tmp$values.myValues<-myValues[[n]] # myGR.List[[n]]<-tmp # } # mycomp.Matrix = epihet::compMatrix(epi.gr = myGR.List, outprefix = NULL, # readNumber = 60, p = 1, # metrics = c("read1","meth1", "pdr", "epipoly", # "shannon","myValues"), # cores = 1, sve = FALSE) ## ----------------------------------------------------------------------------- GR.Object = epihet::readGR(files = files, ids = ids, n = 3) ## ----------------------------------------------------------------------------- summary = epihet::summarize(gr1 = GR.List[[1]], gr2 = GR.List[[2]], value1 = 'pdr', value2 = 'epipoly', cutoff1 = 10, cutoff2 = 60) ## ----------------------------------------------------------------------------- subtype = data.frame(Type= c(rep('CEBPA_sil', 2), rep('Normal', 2)), row.names = names(GR.List),stringsAsFactors = FALSE) ## ----results='hide'----------------------------------------------------------- epihet::epiBox(compare.matrix = comp.Matrix, value = 'epipoly', type = subtype, box.colors = NULL, add.points = FALSE, points.colors = NULL, pdf.height = 4, pdf.width = 4, sve = TRUE) ## ----------------------------------------------------------------------------- pmap = epihet::epiMap(compare.matrix = comp.Matrix, value = 'epipoly',annotate = subtype, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete",annotate.colors = NA, color= colorRampPalette(c("blue","white","red"))(1000), loci.percent = 1, show.rows = FALSE, show.columns = TRUE, font.size = 15, pdf.height = 10, pdf.width = 10, sve = TRUE) ## ----------------------------------------------------------------------------- box.colors=c("orange","forestgreen") names(box.colors)=c("CEBPA_sil","Normal") annotate.colors = list(Type=box.colors) ## ----message=FALSE------------------------------------------------------------ suppressPackageStartupMessages(library(ggfortify)) epihet::epiPCA(compare.matrix = comp.Matrix, value = 'epipoly', type = subtype, points.colors = NULL, frames = FALSE, frames.colors = NULL, probability = FALSE, pdf.height = 4, pdf.width = 5, sve = TRUE) ## ----results='hide'----------------------------------------------------------- set.seed(42) epihet::epiTSNE(compare.matrix = comp.Matrix, value = 'epipoly', type = subtype, points.colors = NULL, theta = 0.5, perplexity = 1, max_iter = 1000, pdf.height = 4, pdf.width = 5, sve = TRUE) ## ----------------------------------------------------------------------------- samples=data.frame(Sample=colnames(comp.Matrix)[1:(length(comp.Matrix)-2)], Genotype=c(rep ("CEBPA_sil", 2), rep ("Normal", 2)), stringsAsFactors = FALSE) rownames(samples)=samples$Sample seed = sample(1:1e+06, 1) set.seed(seed) diff.het.matrix = epihet::diffHet(compare.matrix = comp.Matrix, value = 'epipoly', group1 = 'CEBPA_sil', group2 = 'Normal', subtype = samples, het.dif.cutoff = 0.20, permutations = 1000, p.adjust.method = 'fdr', cores = 1) ## ----results='hide'----------------------------------------------------------- data(diffhetmatrix,package="epihet") epihet::epiMA(pval.matrix = diffhetmatrix, padjust.cutoff = 0.05, pch = 19, sve = TRUE,pointsize=1.5) ## ----results='hide'----------------------------------------------------------- suppressPackageStartupMessages(library(GenomicRanges)) suppressPackageStartupMessages(library(doParallel)) registerDoParallel(cores=1) data(sharedmatrix,package="epihet") data(DEH,package = "epihet") data(datTraits,package = "epihet") data(promoter,package = "epihet") classes=data.frame(Sample= c(colnames(sharedmatrix)[1:(length(sharedmatrix)-2)], paste("N",1:14,sep = "-")),group=c(rep("CEBPA_sil",6), rep("Normal",14)),stringsAsFactors = FALSE) rownames(classes)=classes$Sample epi.network=epihet::epiNetwork(node.type = "gene",DEH,sharedmatrix, value = "epipoly",group="CEBPA_sil", subtype=classes,datTraits = datTraits, promoter,networktype = "signed", method = "pearson",prefix="epipoly", mergeCutHeight = 0.25,minModuleSize = 30) ## ----results='hide'----------------------------------------------------------- load("epipoly-block.1.RData") module.topology=epihet::moduleVisual(TOM, value.matrix=epi.network$epimatrix, moduleColors=epi.network$module$color, mymodule="turquoise",cutoff=0.02, prefix='CEBPA_sil_epipoly',sve = TRUE) ## ----results='hide', message=FALSE, warning=FALSE----------------------------- suppressPackageStartupMessages(library(clusterProfiler)) gene=unique(epi.network$module$gene) entrez=bitr(gene,fromType = "REFSEQ",toType = "ENTREZID", OrgDb = "org.Hs.eg.db") genelist=epi.network$module head(genelist) genelist=merge(genelist,entrez,by.x="gene",by.y="REFSEQ") genelist=unique(genelist[,c(4,2,3)]) head(genelist) pathway = epihet::epiPathway(genelist,cutoff = 0.05,showCategory=8, prefix="CEBPA_sil",pdf.height = 10, pdf.width = 10) ## ----results='hide'----------------------------------------------------------- data(DEG,package = "epihet") data(background,package = "epihet") module.annotation=epihet::moduleAnno(DEG$refseq,background$gene, module.gene=epi.network$module, cutoff=0.1,adjust.method = "fdr", prefix='epipoly',pdf.height = 5, pdf.width = 5, sve = TRUE) ## ----results='hide'----------------------------------------------------------- data(modulesil,package = "epihet") data(moduledm,package = "epihet") sim.score=epihet::moduleSim(module.subtype1=modulesil, module.subtype2=moduledm, pdf.height = 3,pdf.width = 3, sve = TRUE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()