## ----style-knitr, eval=TRUE, echo=FALSE,warning=FALSE, results="asis"------ #library("BiocStyle") BiocStyle::latex() ## ----setup, include=FALSE, cache=FALSE, echo=F------------------------------------------ library(knitr) library(showtext) opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold', fig.showtext=TRUE) options(replace.assign=TRUE,width=90) options(bitmapType="cairo") ## ----citatation------------------------------------------------------------------------- citation(package='coMET') ## ----installPackages,eval=FALSE--------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("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("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----------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install(version = "devel") # BiocManager::install("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',fig.width=7, fig.height=7,warning=FALSE---- 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', type_stacking="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',fig.width=7, fig.height=7 ,warning=FALSE---- 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' ,warning=FALSE------------------------ # 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) # # #Data no more available in UCSC (from September 2015) # 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',fig.width=7, fig.height=7 ,warning=FALSE---- 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' ,warning=FALSE-------------------- # 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(gen, 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',fig.width=7, fig.height=7 ,warning=FALSE---- 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' ,warning=FALSE------------------ # 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(gen, 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' ,warning=FALSE--------------------- 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,warning=FALSE------------------------------------------------------------ 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 ,warning=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 ,warning=FALSE-------------------------------------- gen <- "hg38" chr <- "chr15" start <- 75011669 end <- 75019876 data(interestgenesENSMBLtrack) plotTracks(interestgenesENSMBLtrack, from=start, to=end) ## ----Roadmap_example1e,eval=FALSE,warning=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") # # #lost file # #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) # listRoadMap <- list(genetrack,promRMtrack,dyaRMtrack) # plotTracks(listRoadMap, chromosome=chr,from=start,to=end) ## ----Roadmap_example1e2,echo=FALSE,warning=FALSE---------------------------------------- chr<-"chr2" start <- 38290160 end <- 38303219 gen<-"hg19" data(promRMtrack) #data(enhRMtrack) data(dyaRMtrack) data(genetrack4RM) #listRoadMap <- list(genetrack,promRMtrack,enhRMtrack,dyaRMtrack) listRoadMap <- list(genetrack,promRMtrack,dyaRMtrack) plotTracks(listRoadMap, chromosome=chr,from=start,to=end) ## ----encore_genes,eval=FALSE,warning=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,warning=FALSE--------------------------------------------- #Genes from GENCODE chr<-3 start <- 132239976 end <- 132541303 gen<-"hg19" data(genesGencodetrack) options(ucscChromosomeNames=FALSE) plotTracks(grtrack, chromosome=chr,from=start,to=end) options(ucscChromosomeNames=TRUE) ## ----encode_example,eval=FALSE,warning=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,warning=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,warning=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,warning=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,warning=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,warning=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,warning=FALSE------------------------------------------------------- data(imprintedGenesGTEx) as.character(unique(imprintedGenesGTEx$Tissue.Name)) as.character(unique(imprintedGenesGTEx$Classification)) ## ----GTEX_example5e,eval=FALSE,warning=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(gen, 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,warning=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) ## ----extract_data_1kb,eval=FALSE,warning=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,eval=FALSE,warning=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,warning=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,warning=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) ## ----session-info, results='asis', echo=FALSE,warning=FALSE----------------------------- toLatex(sessionInfo()) ## ----Development, eval=FALSE,echo=FALSE,warning=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/ --enable-R-shlib=yes # # # # sudo make # # # # sudo make check # # # # sudo make install # # # # if need to recompile, do "sudo make uninstall" "sudo make clean" and rerun from ./configure line https://stackoverflow.com/questions/28096239/how-to-configure-r-3-1-2-with-enable-r-shlib # # # # sudo R # # # # #Need to have the last version of Bioconductor and BiocCheck # # #Need to update under Rdev # # remove.packages("BiocManager") # # if (!requireNamespace("BiocManager", quietly=TRUE)) # # install.packages("BiocManager") # # # # #Need to update different packages associated with coMET # # BiocManager::install("coMET") # # # # #Go to the parent folder of the package # # # To create the manual documentation, need to run # # # need to be the folder parent of coMET # # cd ../ # # R-devel CMD Rd2pdf --pdf coMET # # # # # Need to build the vignette # # cd coMET/vignettes # # R-devel CMD Sweave --engine=knitr::knitr --pdf coMET.Rnw # # R-devel CMD texi2dvi --pdf coMET.tex # # R-devel CMD pdflatex coMET.tex # # # # #Need to build the new package # # to addd some parameters for R CMD build/ check/install https://support.rstudio.com/hc/en-us/articles/200486518-Customizing-Package-Build-Options # # # Need to be in the folder parent of coMET # # cd ../../ # # 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 # # # # #Need to install if the new package follow the rules of R # # R-devel CMD INSTALL coMET # # # # #Need to check the examples in R after building and checking # # # Need to correct any examples that fail # # example for the function comet # # R>library(coMET) # # R>example(comet) # # # # #To check if the new package follow the rules from bioconductor # # R-devel CMD BiocCheckdev3.3 coMET # # # To install the new package # # R-devel CMD INSTALL coMET # # # Authors@R: c(person("Tiphaine C.","Martin", role=c("aut","cre"),email="tiphaine.martin@mssm.edu), # # person("Thomas","Hardiman",role=c("aut")), # # person("Idil","Yet",role=c("aut")), # # person("Pei-Chien","Tsai",role=c("aut")), # # person("Jordana T.","Bell",role=c("aut"))) # # #other version of R with Rstudio # #https://support.rstudio.com/hc/en-us/articles/200486138-Changing-R-versions-for-RStudio-desktop #