IVAS (version 1.4.0)

saveBplot: Save boxplots

Description

Save boxplots

Usage

saveBplot(sig.sqtl = NULL, expdata = NULL, snpdata = NULL,
snplocus = NULL, GTFdata = NULL, outdir = NULL)

Arguments

sig.sqtl

A matrix of significant SQTLs from the sqtlfinder function

expdata

Dataframe of expression data.

snpdata

Dataframe of genotype data.

snplocus

Locus of SNP markers in the snpdata.

GTFdata

The transcriptDb object in the GnomicFeatures package.

outdir

A directory saving boxplots

Value

This function draws the boxplot

See Also

boxplot

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
data(samplesnplocus)
data(sampleexp)
data(samplesnp)
filtered.txdb <- chrseparate(sample.Txdb,19)
trans.exon.range <- exonsBy(filtered.txdb,by="tx")
trans.intron.range <- intronsByTranscript(filtered.txdb)
txTable <- select(filtered.txdb, keys=names(trans.exon.range),
columns=c("TXID","TXNAME","GENEID","TXSTART","TXEND"), keytype="TXID")
ch.snp.locus <- as.matrix(samplesnplocus[samplesnplocus[,2] == 19,])
ch.snps <- matrix(ch.snp.locus[is.element(ch.snp.locus[,1],rownames(samplesnp)),],ncol=3,byrow=FALSE)
ch.snps.range <- GRanges(seqnames=Rle(19),ranges=IRanges(start=as.integer(ch.snps[,3]),
end=as.integer(ch.snps[,3])),metadata=ch.snps[,1])
Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)
overlapsnp <- findOversnp(Altvalue,ch.snps.range)
sqtl.result <- sqtlfinder(Altvalue,overlapsnp,sampleexp,samplesnp,"lm")
saveBplot(sqtl.result,sampleexp,samplesnp,samplesnplocus,filtered.txdb,"./result")