ASvisualization {IMAS} | R Documentation |
This function makes a pdf file consisting of plots for results in the ASdb object.
ASvisualization(ASdb,CalIndex=NULL,txTable=NULL,exon.range=NULL,snpdata=NULL, snplocus=NULL,methyldata=NULL,methyllocus=NULL,GroupSam=NULL, ClinicalInfo=NULL,out.dir=NULL)
ASdb |
A ASdb object. |
CalIndex |
An index number in the ASdb object which will be tested in this function. |
txTable |
A data frame of transcripts including transcript IDs, Ensembl gene names, Ensembl transcript names, transcript start sites, and transcript end sites. |
exon.range |
A list of GRanges objects including total exon ranges in each transcript resulted from the |
snpdata |
A data frame of genotype data. |
snplocus |
A data frame consisting of locus information of SNP markers in the snpdata. |
methyldata |
A data frame consisting of methylation levels. |
methyllocus |
A data frame consisting of methylation locus. |
GroupSam |
A list object of a group of each sample. |
ClinicalInfo |
A data frame consisting of a path of bam file and identifier of each sample. |
out.dir |
An output directory |
This function makes pdf for plots.
Seonggyun Han, Younghee Lee
data(sampleGroups) data(samplemethyl) data(samplemethyllocus) data(samplesnp) data(samplesnplocus) data(sampleclinical) data(bamfilestest) ext.dir <- system.file("extdata", package="IMAS") samplebamfiles[,"path"] <- paste(ext.dir,"/samplebam/",samplebamfiles[,"path"],".bam",sep="") sampleDB <- system.file("extdata", "sampleDB", package="IMAS") transdb <- loadDb(sampleDB) ASdb <- Splicingfinder(transdb,Ncor=1) ASdb <- ExonsCluster(ASdb,transdb) ASdb <- RatioFromReads(ASdb,samplebamfiles,"paired",50,40,3,CalIndex="ES3") ASdb <- sQTLsFinder(ASdb,samplesnp,samplesnplocus,method="lm") ASdb <- CompGroupAlt(ASdb,GroupSam,CalIndex="ES3") ASdb <- MEsQTLFinder(ASdb,sampleMedata,sampleMelocus,CalIndex="ES3",GroupSam=GroupSam,out.dir=NULL) Sdb <- ClinicAnalysis(ASdb,Clinical.data,CalIndex="ES3",out.dir=NULL) exon.range <- exonsBy(transdb,by="tx") sel.cn <- c("TXCHROM","TXNAME","GENEID","TXSTART","TXEND","TXSTRAND") txTable <- select(transdb, keys=names(exon.range),columns=sel.cn,keytype="TXID") ASvisualization(ASdb,CalIndex="ES3",txTable,exon.range,samplesnp,samplesnplocus, sampleMedata,sampleMelocus,GroupSam,Clinical.data,out.dir="./")