IVAS (version 1.4.0)

sqtlfinder: Find SQTLs.

Description

Find significant SNPs using the calSignificant function.

Usage

sqtlfinder(altInvalue = NULL, overapvalue = NULL, expdata = NULL, snpdata = NULL, method = NULL)

Arguments

altInvalue

A list data set from the findAlternative function.

overapvalue

A matrix data with SNPs in the flanking introns of alternative exons and ranges of those SNPs from findOversnp function.

expdata

Expression data of samples.

snpdata

Genotype data of samples.

method

The option for statistical models and boxplot.("lm" : analysis using linear regression model, "glm" : analysis using generalized linear mixed model, "both" : "lm" and "glm",and "boxplot" : for writing boxplot).

Value

The lm or glm method returns matrix data including SNP markers ID, chromosome number, alternative exons range, intron ranges, alternative type, P value, information of differential median values of expression ratio among genotypes ("sig" if differential median > 0.1 and "not sig" otherwise), a gene name, methods ("lm" or "glm"),and strand information of the gene. The boxplot method returns matrix data with relative ratio values and genotypes of samples.

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")