findpeaks.traits: List Traits with QTLs at genomic positions

In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description

For a given vector of positions, list traits that map to those positions

Usage

findpeaks.traits(chr, pos, sigpos.out, maxlod.out, peaks.out, win = 5)

Arguments

chr	Character vector of chromosomes, length equal to pos
pos	Numeric vector of positions, on chromosomes listed in chr
sigpos.out	List of positions with significant LOD scores from maxlod.sigpos function
maxlod.out	Optional list output from maxlod function
peaks.out	Optional list output from peaks function
win	Numeric value for window size; trait positions with significant LOD scores within +/- 1/2 win of chr, pos are output

Value

Output is a data.frame with values:

index	Index of chr/pos vector
chr	Chromosome
pos	Position on Chromosome
id	Trait ID, from cross phenotypes
peak.pos	Position of significant maximum LOD score, based on output from maxlod.sigpos
lod	if maxlod dataset is provided, maximum LOD score for traits is included
cis	if peaks dataset is provided, identifier for CIS trait is provided: cis=1 is CIS trait, based on peaks definition, 0 if trans, and NA if unknown

Note

Use in conjunction with findpeaks

Author(s)

Karl W. Broman and Aimee Teo Broman

Examples

data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)

scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")
maxlod.f2 <- maxlod(scan.f2)
sigpos.f2 <- maxlod.sigpos(maxlod.f2,sig.lod=3)

## Random position ##
findpeaks.traits(chr=c("5","1"),pos=c(36,87),sigpos.f2)

## Use findpeaks() ##
n.f2 <- neqtl(sigpos.f2,chr=scan.f2[,1],pos=scan.f2[,2],win=5)
x <- findpeaks(n.f2)

findpeaks.traits(sigpos.f2,chr=x$chr,pos=x$pos)

atbroman/neqtl documentation built on May 10, 2019, 2:08 p.m.