LDheatmap (version 1.0-6)

LDheatmap.addRecombRate: Add recombination rate plot to an LD heat map.

Description

Retrieve average rates of recombination from the deCODE genetic map from the UCSC Genome Browser and add them to an LDheatmap object.

Usage

LDheatmap.addRecombRate(LDheatmap, chromosome, genome = NULL, recombRateLocation = 0.02,
view = "dense")

Arguments

LDheatmap

An object of class LDheatmap.

chromosome

A character string that identifies the chromosome.

genome

The genome assembly to use. The default is the most recent human genome assembly on the UCSC Genome Browser.

recombRateLocation

The plot distance from the LD heat map gene map.

view

Display mode. Possible values are "dense" (the default), "squish", "pack" and "full".

Value

An object of class LDheatmap given as an argument, with the grob LDheatmapGrob modified to inclue the "recombRate" child grob.

References

http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=recombRate

See Also

LDheatmap, recombRate

Examples

# NOT RUN {
data(GIMAP5.CEU) 
ll<-LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position,flip=TRUE)
# Add recombination rate plot
ll_recomb <- LDheatmap.addRecombRate(ll, chr="chr7", genome="hg18")
# }