gap (version 1.5-1)

qtlClassifier: A QTL cis/trans classifier

Description

The function obtains QTL (simply called SNP here) cis/trans classification based on gene positions.

Usage

qtlClassifier(geneSNP, SNPPos, genePos, radius)

Value

It returns a geneSNP-prefixed data.frame with the following columns,

geneChrom

gene chromosome

geneStart

gene start

geneEnd

gene end

SNPChrom

pQTL chromosome

SNPPos

pQTL position

Type

cis/trans labels

Arguments

geneSNP

data.frame with columns on gene, SNP and biomarker (e.g., expression, protein).

SNPPos

data.frame containing SNP, chromosome and position.

genePos

data.frame containing gene, chromosome, start and end positions.

radius

flanking distance.

See Also

cis.vs.trans.classification

Examples

if (FALSE) {
  merged <- read.delim("INF1.merge",as.is=TRUE)
  hits <- merge(merged[c("CHR","POS","MarkerName","prot","log10p")],
                inf1[c("prot","uniprot")],by="prot")
  names(hits) <- c("prot","Chr","bp","SNP","log10p","uniprot")

  options(width=200)
  geneSNP <- merge(hits[c("prot","SNP","log10p")],
                   inf1[c("prot","gene")],by="prot")[c("gene","SNP","prot","log10p")]
  SNPPos <- hits[c("SNP","Chr","bp")]
  genePos <- inf1[c("gene","chr","start","end")]
  cvt <- qtlClassifier(geneSNP,SNPPos,genePos,1e6)
  cvt
  cistrans <- cis.vs.trans.classification(hits,inf1,"uniprot")
  cis.vs.trans <- with(cistrans,data)
  cistrans.check <- merge(cvt[c("gene","SNP","Type")],cis.vs.trans[c("p.gene","SNP","cis.trans")],
                          by.x=c("gene","SNP"),by.y=c("p.gene","SNP"))
  with(cistrans.check,table(Type,cis.trans))
}