findpeaks.traits: List Traits with QTLs at genomic positions

Description Usage Arguments Value Note Author(s) Examples

Description

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

Usage

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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

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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.