ASvisualization: Visualize the results of the ASdb object.

In IMAS: Integrative analysis of Multi-omics data for Alternative Splicing

Description

This function makes a pdf file consisting of plots for results in the ASdb object.

Usage

    ASvisualization(ASdb,CalIndex=NULL,txTable=NULL,exon.range=NULL,snpdata=NULL,
    snplocus=NULL,methyldata=NULL,methyllocus=NULL,GroupSam=NULL,
    ClinicalInfo=NULL,out.dir=NULL)

Arguments

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 exonsBy function in GenomicFeatures.
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

Value

This function makes pdf for plots.

Author(s)

Seonggyun Han, Younghee Lee

Examples

    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="./")

IMAS documentation built on Nov. 8, 2020, 7:48 p.m.