xaxisloc.scanone: Get x-axis locations in scanone plot

In kbroman/qtl: Tools for Analyzing QTL Experiments

Get x-axis locations in scanone plot

Description

Get x-axis locations for given cM positions on given chromosomes in a plot from plot.scanone)

Usage

xaxisloc.scanone(out, thechr, thepos, chr, gap=25)

Arguments

out	An object of class "scanone", as output by scanone. This must be identical to what was used in the call to plot.scanone.
thechr	Chromosome IDs at which x-axis locations are to be determined.
thepos	Chromosome positions at which x-axis locations are to be determined.
chr	Optional vector specifying which chromosomes were plotted. This must be identical to what was used in the call to plot.scanone.
gap	Gap separating chromosomes (in cM). This must be identical to what was used in the call to plot.scanone.

Details

This function allows you to identify the x-axis locations in a plot of genome scan results, produced by plot.scanone. This is useful for adding annotations, such as text or arrows.

The arguments out, chr, and gap must match what was used in the call to plot.scanone.

The arguments thechr and thepos indicate the genomic positions for which x-axis locations are desired. If they both have length > 1, they must have the same length. If one has length > 1 and one has length 1, the one with length 1 is expanded to match.

Value

A numeric vector of x-axis locations.

Author(s)

Karl W Broman, [e-mail]

See Also

plot.scanone, add.threshold

Examples

data(hyper)

hyper <- calc.genoprob(hyper)
out <- scanone(hyper, method="hk")
plot(out, chr=c(1, 4, 6, 15))

# add arrow and text to indicate peak LOD score
mxout <- max(out)
x <- xaxisloc.scanone(out, mxout$chr, mxout$pos, chr=c(1,4,6,15))
arrows(x+30, mxout$lod, x+5, mxout$lod, len=0.1, col="blue")
text(x+35, mxout$lod, "the peak", col="blue", adj=c(0, 0.5))

kbroman/qtl documentation built on Aug. 26, 2024, 12:33 a.m.