qtlClassifier: A QTL cis/trans classifier

In gap: Genetic Analysis Package

A QTL cis/trans classifier

Description

A QTL cis/trans classifier

Usage

qtlClassifier(geneSNP, SNPPos, genePos, radius)

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.

Details

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

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.

Note

This is adapted from iBMQ/eqtlClassifier as an xQTL (x=e, p, me, ...) classifier.

See Also

cis.vs.trans.classification

Examples

## Not run: 
  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))

## End(Not run)

gap documentation built on Aug. 26, 2023, 5:07 p.m.