Nothing
inst/doc/coMET.R
In coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
## ----style-knitr, eval=TRUE, echo=FALSE,warning=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---------------------------------------------------------
# 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")
#
# 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,warning=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,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
#
Try the coMET package in your browser
Any scripts or data that you put into this service are public.
coMET documentation built on Nov. 8, 2020, 5 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ----style-knitr, eval=TRUE, echo=FALSE,warning=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---------------------------------------------------------
# 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")
#
# 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,warning=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,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
#
Try the coMET package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.