findpeaks: Locates positions of high numbers of eQTL
In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description Usage Arguments Value Author(s) See Also Examples

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

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

`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)

data.frame of chr and pos of peak positions

Karl W. Broman and Aimee Teo Broman

findpeaks.traits

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)