View source: R/LDheatmap.addRecombRate.R
LDheatmap.addRecombRate | R Documentation |
Retrieve average rates of recombination from the deCODE genetic map from the UCSC Genome Browser and add them to an LDheatmap object.
LDheatmap.addRecombRate(LDheatmap, chromosome, genome = NULL, recombRateLocation = 0.02, view = "dense")
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 |
An object of class LDheatmap given as an argument, with the grob
LDheatmapGrob
modified to inclue the "recombRate"
child grob.
Sigal Blay <sblay@sfu.ca>
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=recombRate
LDheatmap
, recombRate
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")
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