findpeaks: Locates positions of high numbers of eQTL

Description Usage Arguments Value Author(s) See Also Examples

Description

Given output from neqtl, finds positions for maximum numbers of eQTL. Will find next highest maximum outside of window from peak, for n.peaks number of maximums

Usage

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findpeaks(neqtl.out, lodcolumn = 1, window = 5, n.peaks = 10)

Arguments

neqtl.out

Output from neqtl function, a scanone object of number of eQTL by position within a window

lodcolumn

Numeric value for which LOD column to use, default is first column

window

Numeric value of window size, greater than or equal to win parameter used in neqtl function, so neighboring maximums will not share transcripts

n.peaks

Number of peaks to find (e.g. for n.peaks=10, the top 10 positions of maximum values)

Value

data.frame of chr and pos of peak positions

Author(s)

Karl W. Broman and Aimee Teo Broman

See Also

findpeaks.traits

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)

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

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