peaks: Proximity of Maximum LOD position to Transcript Location
In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description Usage Arguments Value Author(s) See Also Examples

Determines distance between position of maximum LOD score and trait position, based on annotation. Assigns CIS/Trans status based on a window size (default=5)

1	peaks(maxlod.out, sigpos.out, annot, win = 5)

`maxlod.out`	Output from `maxlod` function
`sigpos.out`	Output from `maxlod.sigpos` function
`annot`	A data.frame consisting of two columns: `chr` (Chromosome name, as a factor, with levels in the same order as the original `scanone` object. Additional levels may be added at the end) and `pos` (Position of trait in the same units as `scanone` object). The rownames should be the trait IDs, same as pheno names in original cross object.
`win`	Window size, in same units as `scanone` object (e.g. cM or Mb)

Returns a list corresponding to the number of chromosomes:

`maxpos`	List of maximum LOD positions, named by trait, with existing location in annotation
`maxlods`	List of maximum LOD scores, named by trait, with existing location in annotation
`maxpos.cis`	List of maximum LOD positions, named by trait, within +/- 1/2 window size of annotation location
`maxpos.vaguelycis`	List of maximum LOD positions, named by trait, on the same chromosome as annotation location
`maxpos.forsuretrans`	List of maximum LOD positions, named by trait, on different chromosome as annotation location
`maxpos.trans`	List of maximum LOD positions, named by trait, outside of +/- 1/2 window size, or on different chromosome of annotation location
`maxlods.cis`	List of maximum LOD scores, named by trait, within +/- 1/2 window size of annotation location
`maxlods.trans`	List of maximum LOD scores, named by trait, outside of +/- 1/2 window size, or on different chromosome of annotation location
`maxpos.trait`	List of annotation positions, named by trait
`peaks`	`data.frame` of traits with maximum lod score (by chromosome) higher than a significance threshold (as defined in `maxlod.sigpos`), columns named "peaks" refer to linkage, columns named "trait" refer to annotation. This object can be used for plotting.

Karl W. Broman and Aimee Teo Broman

plotpeaks

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)

## Fake annotation ##
data(fake.annot)

peaks.f2 <- peaks(maxlod.f2,sigpos.f2,fake.annot)