## ----style, eval=TRUE, echo=FALSE,results="asis"------------------------- #library("BiocStyle") BiocStyle::latex() ## ----setup, include=FALSE, cache=FALSE, echo=F--------------------------- library(knitr) opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold') options(replace.assign=TRUE,width=90) ## ----citatation---------------------------------------------------------- citation(package='coMET') ## ----installPackages,eval=FALSE------------------------------------------ ## source("http://bioconductor.org/biocLite.R") ## biocLite("coMET") ## ----installPackagesdepend,eval=FALSE------------------------------------ ## install.packages("psych") ## install.packages("corrplot") ## install.packages("colortools") ## ----dd,echo=FALSE,eval=FALSE-------------------------------------------- ## require("hash") ## require("grid") ## require("grDevices") ## require("biomaRt") ## require("Gviz") ## require("ggbio") ## require("rtracklayer") ## require("GenomicRanges") ## require("colortools") ## require("gridExtra") ## require("ggplot2") ## require("trackViewer") ## require("psych") ## ## rdir <- system.file("R", package="coMET",mustWork=TRUE) ## source(file.path(rdir, "AnalyseFile.R")) ## source(file.path(rdir, "BiofeatureGraphics.R")) ## source(file.path(rdir, "comet.R")) ## source(file.path(rdir, "cometWeb.R")) ## source(file.path(rdir, "DrawPlot.R")) ## source(file.path(rdir, "GeneralMethodComet.R")) ## ----loadPackages, eval=TRUE--------------------------------------------- library("coMET") ## ----findHel, eval=FALSE------------------------------------------------- ## ?comet ## ?comet.web ## ?comet.list ## ----installPackages_develbioc,eval=FALSE-------------------------------- ## source("http://bioconductor.org/biocLite.R") ## biocLite("coMET") ## ----installPackages_develversion,eval=FALSE----------------------------- ## install.packages("YourPath/coMET_YourVersion.tar.gz",repos=NULL,type="source") ## ##This is an example ## install.packages("YourPath/coMET_0.99.9.tar.gz",repos=NULL,type="source") ## ----Filedata------------------------------------------------------------ extdata <- system.file("extdata", package="coMET",mustWork=TRUE) infofile <- file.path(extdata, "cyp1b1_infofile.txt") data_info <-read.csv(infofile, header = TRUE, sep = "\t", quote = "") head(data_info) ## ----expMatrix----------------------------------------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) infoexp <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt") data_infoexp <-read.csv(infoexp, header = TRUE, sep = "\t", quote = "") head(data_infoexp) ## ----corrMatrix---------------------------------------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) corfile <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") data_cor <-read.csv(corfile, header = TRUE, sep = "\t", quote = "") data_cor[1:6,1:6] ## ----configMatrix-------------------------------------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver_Grch38.txt") data_config <-read.csv(configfile, quote = "", sep="\t", header=FALSE) data_config ## ----cometwebPlotText, eval=FALSE, fig.keep='last'----------------------- ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## myinfofile <- file.path(extdata, "cyp1b1_infofile_Grch38.txt") ## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region_Grch38.txt") ## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") ## configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver_Grch38.txt") ## comet.web(config.file=configfile, mydata.file=myinfofile, ## cormatrix.file=mycorrelation ,mydata.large.file=myexpressfile, ## print.image=FALSE,verbose=FALSE) ## ----cometwebPlot, echo=FALSE, fig.keep='last'--------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) myinfofile <- file.path(extdata, "cyp1b1_infofile_Grch38.txt") myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region_Grch38.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver_Grch38.txt") comet.web(config.file=configfile, mydata.file=myinfofile, cormatrix.file=mycorrelation ,mydata.large.file=myexpressfile, print.image=FALSE,verbose=FALSE) ## ----cometPlotText, eval=FALSE, fig.keep='last'-------------------------- ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt") ## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") ## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt") ## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") ## ## chrom <- "chr2" ## start <- 38290160 ## end <- 38303219 ## gen <- "hg19" ## strand <- "*" ## ## BROWSER.SESSION="UCSC" ## mySession <- browserSession(BROWSER.SESSION) ## genome(mySession) <- gen ## ## genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE) ## snptrack <- snpBiomart_ENSEMBL(gen,chrom, start, end, dataset="hsapiens_snp_som",showId=FALSE) ## cpgIstrack <- cpgIslands_UCSC(gen,chrom,start,end) ## ## prombedFilePath <- file.path(extdata, "/RoadMap/regions_prom_E063.bed") ## promRMtrackE063<- DNaseI_RoadMap(gen,chrom,start, end, prombedFilePath, ## featureDisplay='promotor', stacking_type="squish") ## ## bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed") ## chromHMM_RoadMapAllE063 <- chromHMM_RoadMap(gen,chrom,start, end, bedFilePath, featureDisplay = "all", colorcase='roadmap15' ) ## ## listgviz <- list(genetrack,snptrack,cpgIstrack,promRMtrackE063,chromHMM_RoadMapAllE063) ## ## comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", ## cormatrix.file=mycorrelation, cormatrix.type="listfile", ## mydata.large.file=myexpressfile, mydata.large.type="listfile", ## tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE) ## ----cometPlotfile, echo=FALSE, fig.keep='last'-------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt") myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") chrom <- "chr2" start <- 38290160 end <- 38303219 gen <- "hg19" strand <- "*" data(geneENSEMBLtrack) data(snpBiomarttrack) data(cpgIslandtrack) data(promRMtrackE063) data(chromHMM_RoadMapAllE063) listgviz <- list(genetrack,snptrack,cpgIstrack,promRMtrackE063,chromHMM_RoadMapAllE063) comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", cormatrix.file=mycorrelation, cormatrix.type="listfile", mydata.large.file=myexpressfile, mydata.large.type="listfile", tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE) ## ----cometPlotmatrix, eval=FALSE, fig.keep='last'------------------------ ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt") ## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") ## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt") ## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") ## ## chrom <- "chr2" ## start <- 38290160 ## end <- 38303219 ## gen <- "hg19" ## strand <- "*" ## ## BROWSER.SESSION="UCSC" ## mySession <- browserSession(BROWSER.SESSION) ## genome(mySession) <- gen ## ## genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE) ## snptrack <- snpBiomart_ENSEMBL(chrom, start, end, dataset="hsapiens_snp_som",showId=FALSE) ## iscatrack <-ISCA_UCSC(gen,chrom,start,end,mySession, table="iscaPathogenic") ## ## listgviz <- list(genetrack,snptrack,iscatrack) ## ## matrix.dnamethylation <- read.delim(myinfofile, header=TRUE, sep="\t", as.is=TRUE, ## blank.lines.skip = TRUE, fill=TRUE) ## matrix.expression <- read.delim(myexpressfile, header=TRUE, sep="\t", as.is=TRUE, ## blank.lines.skip = TRUE, fill=TRUE) ## cormatrix.data.raw <- read.delim(mycorrelation, sep="\t", header=TRUE, as.is=TRUE, ## blank.lines.skip = TRUE, fill=TRUE) ## ## listmatrix.expression <- list(matrix.expression) ## listcormatrix.data.raw <- list(cormatrix.data.raw) ## comet(config.file=configfile, mydata.file=matrix.dnamethylation, ## mydata.type="dataframe",cormatrix.file=listcormatrix.data.raw, ## cormatrix.type="listdataframe",cormatrix.sig.level=0.05, ## cormatrix.conf.level=0.05, cormatrix.adjust="BH", ## mydata.large.file=listmatrix.expression, mydata.large.type="listdataframe", ## fontsize.gviz =12, ## tracks.gviz=listgviz,verbose=FALSE, print.image=FALSE) ## ----cometPlotMatrix, echo=FALSE, fig.keep='last'------------------------ extdata <- system.file("extdata", package="coMET",mustWork=TRUE) configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt") myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") #configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" chrom <- "chr2" start <- 38290160 end <- 38303219 gen <- "hg19" strand <- "*" data(geneENSEMBLtrack) data(snpBiomarttrack) data(ISCAtrack) listgviz <- list(genetrack,snptrack,iscatrack) matrix.dnamethylation <- read.delim(myinfofile, header=TRUE, sep="\t", as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE) matrix.expression <- read.delim(myexpressfile, header=TRUE, sep="\t", as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE) cormatrix.data.raw <- read.delim(mycorrelation, sep="\t", header=TRUE, as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE) listmatrix.expression <- list(matrix.expression) listcormatrix.data.raw <- list(cormatrix.data.raw) comet(config.file=configfile, mydata.file=matrix.dnamethylation, mydata.type="dataframe",cormatrix.file=listcormatrix.data.raw, cormatrix.type="listdataframe",cormatrix.sig.level=0.05, cormatrix.conf.level=0.05, cormatrix.adjust="BH", mydata.large.file=listmatrix.expression, mydata.large.type="listdataframe", fontsize.gviz =12, tracks.gviz=listgviz,verbose=FALSE, print.image=FALSE) ## ----cometPlotNopvalText, eval=FALSE, fig.keep='last'-------------------- ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## configfile <- file.path(extdata, "config_cyp1b1_zoom_4cometnopval.txt") ## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") ## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") ## ## chrom <- "chr2" ## start <- 38290160 ## end <- 38303219 ## gen <- "hg19" ## strand <- "*" ## ## genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=FALSE) ## snptrack <- snpBiomart_ENSEMBL(chrom, start, end, ## dataset="hsapiens_snp_som",showId=FALSE) ## strutrack <- structureBiomart_ENSEMBL(chrom, start, end, ## strand, dataset="hsapiens_structvar_som") ## clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end) ## clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end) ## gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end) ## geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end) ## ## listgviz <- list(genetrack,snptrack,strutrack,clinVariant, ## clinCNV,gwastrack,geneRtrack) ## comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", ## cormatrix.file=mycorrelation, cormatrix.type="listfile", ## fontsize.gviz =12, ## tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE) ## ----cometPlot_nopval, echo=FALSE, fig.keep='last'----------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) configfile <- file.path(extdata, "config_cyp1b1_zoom_4cometnopval.txt") #configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") chrom <- "chr2" start <- 38290160 end <- 38303219 gen <- "hg19" strand <- "*" data(geneENSEMBLtrack) data(snpBiomarttrack) data(strucBiomarttrack) data(ClinVarCnvTrack) data(clinVarMaintrack) data(GWASTrack) data(GeneReviewTrack) listgviz <- list(genetrack,snptrack,strutrack,clinVariant, clinCNV,gwastrack,geneRtrack) comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", cormatrix.file=mycorrelation, cormatrix.type="listfile", fontsize.gviz =12, tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE) ## ----cometPlotNomatrixtext, eval=FALSE, fig.keep='last'------------------ ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## configfile <- file.path(extdata, "config_cyp1b1_zoom_4nomatrix.txt") ## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") ## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") ## ## chrom <- "chr2" ## start <- 38290160 ## end <- 38303219 ## gen <- "hg19" ## strand <- "*" ## ## genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=FALSE) ## snptrack <- snpBiomart_ENSEMBL(chrom, start, end, ## dataset="hsapiens_snp_som",showId=FALSE) ## strutrack <- structureBiomart_ENSEMBL(chrom, start, end, ## strand, dataset="hsapiens_structvar_som") ## clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end) ## clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end) ## gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end) ## geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end) ## ## listgviz <- list(genetrack,snptrack,strutrack,clinVariant, ## clinCNV,gwastrack,geneRtrack) ## comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", ## cormatrix.file=mycorrelation, cormatrix.type="listfile", ## fontsize.gviz =12, font.factor=3, ## tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE) ## ----cometPlot_nomatrix, echo=FALSE, fig.keep='last'--------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) configfile <- file.path(extdata, "config_cyp1b1_zoom_4nomatrix.txt") myinfofile <- file.path(extdata, "cyp1b1_infofile.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") chrom <- "chr2" start <- 38290160 end <- 38303219 gen <- "hg19" strand <- "*" data(geneENSEMBLtrack) data(snpBiomarttrack) data(strucBiomarttrack) data(ClinVarCnvTrack) data(clinVarMaintrack) data(GWASTrack) data(GeneReviewTrack) listgviz <- list(genetrack,snptrack,strutrack,clinVariant, clinCNV,gwastrack,geneRtrack) comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file", cormatrix.file=mycorrelation, cormatrix.type="listfile", fontsize.gviz =12, font.factor=3, tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE) ## ----cometlist----------------------------------------------------------- extdata <- system.file("extdata", package="coMET",mustWork=TRUE) mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") myoutput <- file.path(extdata, "cyp1b1_res37_cormatrix_list_BH05.txt") comet.list(cormatrix.file=mycorrelation,cormatrix.method = "spearman", cormatrix.format= "raw", cormatrix.conf.level=0.05, cormatrix.sig.level= 0.05, cormatrix.adjust="BH", cormatrix.type = "listfile", cormatrix.output=myoutput, verbose=FALSE) listcorr <- read.csv(myoutput, header = TRUE, sep = "\t", quote = "") dim(listcorr) head(listcorr) ## ----GenesAndTranscript,eval=FALSE--------------------------------------- ## gen <- "hg38" ## chr <- "chr15" ## start <- 75011669 ## end <- 75019876 ## interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good")) ## interestcolor <- list("bad"="red", "good"="green") ## ## interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,interestfeatures, ## interestcolor,showId=TRUE) ## plotTracks(interestgenesENSMBLtrack, from=start, to=end) ## ----GenesAndTranscript2,echo=FALSE-------------------------------------- gen <- "hg38" chr <- "chr15" start <- 75011669 end <- 75019876 data(interestgenesENSMBLtrack) plotTracks(interestgenesENSMBLtrack, from=start, to=end) ## ----Roadmap_example1e,eval=FALSE---------------------------------------- ## chr<-"chr2" ## start <- 38290160 ## end <- 38303219 ## gen<-"hg19" ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## prombedFilePath <- file.path(extdata, "/RoadMap/regions_prom_E001.bed") ## ## promRMtrack<- DNaseI_RoadMap(gen,chr,start, end, prombedFilePath, ## featureDisplay='promotor', type_stacking="squish") ## ## enhbedFilePath <- file.path(extdata, "/RoadMap/regions_enh_E001.bed") ## ## enhRMtrack<- DNaseI_RoadMap(gen,chr,start, end, enhbedFilePath, ## featureDisplay='enhancer', type_stacking="squish") ## ## dyabedFilePath <- file.path(extdata, "/RoadMap/regions_dyadic_E001.bed") ## ## dyaRMtrack<- DNaseI_RoadMap(gen,chr,start, end, dyabedFilePath, ## featureDisplay='dyadic', type_stacking="squish") ## ## genetrack <-genes_ENSEMBL(gen,chr,start,end,showId=TRUE) ## ## listRoadMap <- list(genetrack,promRMtrack,enhRMtrack,dyaRMtrack) ## plotTracks(listRoadMap, chromosome=chr,from=start,to=end) ## ----Roadmap_example1e2,echo=FALSE--------------------------------------- chr<-"chr2" start <- 38290160 end <- 38303219 gen<-"hg19" data(promRMtrack) data(enhRMtrack) data(dyaRMtrack) data(genetrack4RM) listRoadMap <- list(genetrack,promRMtrack,enhRMtrack,dyaRMtrack) plotTracks(listRoadMap, chromosome=chr,from=start,to=end) ## ----encore_genes,eval=FALSE--------------------------------------------- ## #Genes from GENCODE ## chr<-3 ## start <- 132239976 ## end <- 132541303 ## gen<-"hg19" ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## gtfFilePath <- file.path(extdata, "/GTEX/gencode.v19.genes.patched_contigs.gtf") ## options(ucscChromosomeNames=FALSE) ## grtrack <- GeneRegionTrack(range=gtfFilePath ,chromosome = chr, start= start, ## end= end, name = "Gencode V19", ## collapseTranscripts=TRUE, showId=TRUE,shape="arrow") ## plotTracks(grtrack, chromosome=chr,from=start,to=end) ## ----encore_genes2,echo=FALSE-------------------------------------------- #Genes from GENCODE chr<-3 start <- 132239976 end <- 132541303 gen<-"hg19" data(genesGencodetrack) plotTracks(grtrack, chromosome=chr,from=start,to=end) ## ----encode_example,eval=FALSE------------------------------------------- ## #TF Chip-seq data ## gen <- "hg19" ## chr<-"chr1" ## start <- 1000 ## end <- 329000 ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## bedFilePath <- file.path(extdata, "ENCODE/motifs1000_matches_ENCODE.txt") ## motif_color <- file.path(extdata, "ENCODE/TFmotifs_colors.csv") ## ## chipTFtrack <- ChIPTF_ENCODE(gen,chr,start, end, bedFilePath, ## featureDisplay=c("AHR::ARNT::HIF1A_1", ## "AIRE_1","AIRE_2","AHR::ARNT_1"), ## motif_color,type_stacking="squish",showId=TRUE) ## ## plotTracks(chipTFtrack, chromosome=chr,from=start,to=end) ## ----encode_example2,echo=FALSE------------------------------------------ #TF Chip-seq data gen <- "hg19" chr<-"chr1" start <- 1000 end <- 329000 data(chipTFtrack) plotTracks(chipTFtrack, from = start, to = end) ## ----GTEX_example1,eval=FALSE-------------------------------------------- ## ## eQTL data ## chr<-"chr3" ## start <- 132239976 ## end <- 132541303 ## gen<-"hg19" ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## bedFilePath <- file.path(extdata, "/GTEX/eQTL_Uterus_Analysis_extract100.snpgenes") ## ## eGTex<- eQTL_GTEx(gen,chr, start, end, bedFilePath, featureDisplay = 'all', ## showId=TRUE, type_stacking="squish", just_group="left" ) ## ## eGTex_SNP<- eQTL_GTEx(gen,chr, start, end, bedFilePath, ## featureDisplay = 'SNP', showId=FALSE, ## type_stacking="dense", just_group="left") ## ## #Genes from ## gtfFilePath <- file.path(extdata, "/GTEX/gencode.v19.genes.patched_contigs.gtf") ## options(ucscChromosomeNames=FALSE) ## grtrack <- GeneRegionTrack(genome="hg19",range=gtfFilePath ,chromosome = chr, ## start= start, end= end, name = "Gencode V19", ## collapseTranscripts=TRUE, showId=TRUE,shape="arrow") ## eGTexTracklist <- list(grtrack,eGTexTrackSNP) ## plotTracks(eGTexTracklist, chromosome=chr,from=start,to=end) ## ----GTEX_example12,echo=FALSE------------------------------------------- ## eQTL data chr<-"chr3" start <- 132239976 end <- 132541303 gen<-"hg19" data(eGTexTrackSNP) data(eGTexTrackall) data(grtrack4eGTex) #Genes from eGTexTracklist <- list(grtrack,eGTexTrackSNP) plotTracks(eGTexTracklist, chromosome=chr,from=start,to=end) ## ----GTEX_example4e,eval=FALSE------------------------------------------- ## ### psiQTL ## chr<-"chr13" ## start <- 52713837 ## end <- 52715894 ## gen<-"hg19" ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## psiQTLFilePath <- file.path(extdata, "/GTEX/psiQTL_Assoc-total.AdiposeTissue.txt") ## ## psiGTex<- psiQTL_GTEx(gen,chr,start, end, psiQTLFilePath, featureDisplay = 'all', ## showId=TRUE, type_stacking="squish",just_group="above" ) ## ## genetrack <-genes_ENSEMBL(gen,chr,start,end,showId=TRUE) ## ## psiTrack <- list(genetrack,psiGTex) ## plotTracks(psiTrack, chromosome=chr,from=start,to=end) ## ----GTEX_example4e2,echo=FALSE------------------------------------------ ### psiQTL chr<-"chr13" start <- 52713837 end <- 52715894 gen<-"hg19" data(psiGTexTrackall) data(genetrack4psiGTEX) psiTrack <- list(genetrack,psiGTexTrackall) plotTracks(psiTrack, chromosome=chr,from=start,to=end) ## ----TEX_example5e1------------------------------------------------------ data(imprintedGenesGTEx) as.character(unique(imprintedGenesGTEx$Tissue.Name)) as.character(unique(imprintedGenesGTEx$Classification)) ## ----GTEX_example5e,eval=FALSE------------------------------------------- ## ### inprinted genes ## chr<- "chr1" ## start <- 7895752 ## end <- 7914572 ## gen<-"hg19" ## ## genesTrack <- genes_ENSEMBL(gen,chr,start,end,showId=TRUE) ## ## allIG <- imprintedGenes_GTEx(gen,chr,start, end, tissues="all", ## classification="imprinted",showId=TRUE) ## ## allimprintedIG <- imprintedGenes_GTEx(chr,start, end, tissues="all", ## classification="imprinted",showId=TRUE) ## ## StomachIG <-imprintedGenes_GTEx(gen,chr,start, end, tissues="Stomach", ## classification="all",showId=TRUE) ## ## PancreasIG <- imprintedGenes_GTEx(gen,chr,start, end, ## tissues="Pancreas", ## classification="all",showId=TRUE) ## PancreasimprintedIG <- imprintedGenes_GTEx(gen,chr,start, end, tissues="Pancreas", ## classification="imprinted",showId=TRUE) ## ## plotTracks(list(genesTrack, allIG, allimprintedIG, ## StomachIG,PancreasIG,PancreasimprintedIG), ## chromosome=chr, from=start, to=end) ## ## ----GTEX_example5e2,echo=FALSE------------------------------------------ ### inprinted genes chr<- "chr1" start <- 7895752 end <- 7914572 gen<-"hg19" genesTrack <- genes_ENSEMBL(gen,chr,start,end,showId=TRUE) data(allIGtrack) data(allimprintedIGtrack) data(StomachIGtrack) data(PancreasIGtrack) data(PancreasimprintedIGtrack) imprintinglist <- list(genesTrack,allIGtrack,allimprintedIGtrack,StomachIGtrack, PancreasIGtrack,PancreasimprintedIGtrack) plotTracks(imprintinglist, from = start, to = end) ## ----GTEX_example3,eval=FALSE,echo=FALSE--------------------------------- ## ## sQTL data ## chr<-3 ## start <- 132239976 ## end <- 132541303 ## gen<-"hg19" ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## ## ### sQTL from Altran methods ## sQTLAFilePath <- file.path(extdata, "/GTEX/sQTL_HeartLeftVentricle.Altrans.FDR05.bestPerLink") ## ## sAGTex<- sQTL_Altrans_GTEx(gen,chr,start, end, ## sQTLAFilePath, featureDisplay = 'all', showId=TRUE, ## type_stacking="squish",just_group="left" ) ## ----extract_data_1kb,eval=FALSE----------------------------------------- ## library('corrplot') ## #Hi-C data ## gen <- "hg19" ## chr<-"chr1" ## start <- 5000000 ## end <- 9000000 ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## bedFilePath <- file.path(extdata, "HiC/chr1_1mb.RAWobserved") ## ## matrix_HiC <- HiCdata2matrix(chr,start, end, bedFilePath) ## cor_matrix_HiC <- cor(matrix_HiC) ## diag(cor_matrix_HiC)<-1 ## corrplot(cor_matrix_HiC, method = "circle") ## ----extract_data_1kb2,echo=FALSE---------------------------------------- library('corrplot') #Hi-C data gen <- "hg19" chr<-"chr1" start <- 5000000 end <- 9000000 data(matrix_HiC_Rao) cor_matrix_HiC <- cor(matrix_HiC_Rao) diag(cor_matrix_HiC)<-1 corrplot(cor_matrix_HiC, method = "circle") ## ----extract_data,eval=FALSE--------------------------------------------- ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## info_HiC <- file.path(extdata, "Human_IMR90_Fibroblast_topological_domains.txt") ## data_info_HiC <-read.csv(info_HiC, header = FALSE, sep = "\t", quote = "") ## ## intrachr_HiC <- file.path(extdata, "Human_IMR90_Fibroblast_Normalized_Matrices.txt") ## data_intrachr_HiC <- read.csv(intrachr_HiC, header = TRUE, sep = "\t", quote = "") ## ## chr_interest <- "chr2" ## start_interest <- "1" ## end_interest <- "160000" ## list_bins <- which(data_info_HiC[,1] == chr_interest & ## data_info_HiC[,2] >= start_interest & ## data_info_HiC[,2] <= end_interest ) ## ## subdata_info_Hic <- data_info_HiC[list_bins,] ## subdata_intrachr_HiC <- data_intrachr_HiC[list_bins,list_bins] ## ## ----FANTOM_example,eval=FALSE------------------------------------------- ## gen <- "hg19" ## chr<- "chr1" ## start <- 6000000 ## end <- 6500000 ## ## extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ## ## ##Enhancer ## enhFantomFile <- file.path(extdata, "/FANTOM/human_permissive_enhancers_phase_1_and_2.bed") ## enhFANTOMtrack <-DNaseI_FANTOM(gen,chr,start, end, enhFantomFile, featureDisplay='enhancer') ## ## ### TFBS motif ## AP1FantomFile <- file.path(extdata, "/FANTOM/Fantom_hg19.AP1_MA0099.2.sites.txt") ## tfbsFANTOMtrack <- TFBS_FANTOM(gen,chr,start, end, AP1FantomFile) ## ----FANTOM_example2,echo=FALSE------------------------------------------ gen <- "hg19" chr<- "chr1" start <- 6000000 end <- 6500000 extdata <- system.file("extdata", package="coMET",mustWork=TRUE) ##Enhancer data(enhFANTOMtrack) ### TFBS motif data(tfbsFANTOMtrack) Fantom5list <- list(enhFANTOMtrack,tfbsFANTOMtrack) plotTracks(Fantom5list, from = start, to = end) ## ----faq0,eval=FALSE----------------------------------------------------- ## genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE) ## ## plotTracks(genetrack) ## ## str(genetrack) ## ----faq1,eval=FALSE----------------------------------------------------- ## genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE) ## ## displayPars(genetrack) ## ----faq2,eval=FALSE----------------------------------------------------- ## comet(config.file = configfile, mydata.file = myinfofile, mydata.format = "file", ## cormatrix.file = mycorrelation, cormatrix.type = "listfile", ## mydata.large.file = mylargedata,mydata.large.type = "listfile", ## tracks.gviz = listGviz, verbose = TRUE, ## print.image=TRUE,fontsize.gviz=10) ## ----faq3,eval=FALSE----------------------------------------------------- ## geneTrack <- refGenesUCSC(gen, chr, start, end, IdType ="name", showId = TRUE) ## ## geneTrackShow <- geneTrack[gene(geneTrack) %in% c("AHRR")] ## ----session-info, results="asis"---------------------------------------- toLatex(sessionInfo()) ## ----Development, eval=FALSE,echo=FALSE---------------------------------- ## #Doc for Shiny Server ## https://www.digitalocean.com/community/tutorials/how-to-set-up-shiny-server-on-ubuntu-14-04 ## ## #Need to have the last version of R associated with Bioconductor in parallele of your original version ## #install from source http://bioconductor.org/developers/how-to/useDevel/ ## mkdir /home/tiphaine/Rdevel2.2/ ## cd Rdevel2.2 ## mkdir tar ## #Extract R source in this latter folder ## ./configure -prefix=/home/tiphaine/Rdevel2.2/ ## ## sudo make ## ## sudo make install ## ## #Need to have the last version of Bioconductor and BiocCheck ## #Need to update under Rdev ## remove.packages("BiocInstaller") ## source("http://bioconductor.org/biocLite.R") ## biocLite("BiocInstaller") ## ## #Need to update different packages associated with coMET ## biocLite("coMET") ## ## #Go to the parent folder of the package ## # To create the manual documentation, need to run ## Rdevel CMD Rd2pdf --pdf coMET ## ## #Need to build the new package ## R-devel CMD build coMET --resave-data --no-build-vignettes ## ## #Need to check if the new package follow the rules of R ## R-devel CMD check coMET ## ## #To check if the new package follow the rules from bioconductor ## R-devel CMD BiocCheckdev3.3 coMET