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

In 321Yan/LDheatmap-testing: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

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.

Author(s)

Sigal Blay <[e-mail]>

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")

## End(Not run)

321Yan/LDheatmap-testing documentation built on July 14, 2019, 2:28 p.m.