LDheatmap.addGenes: Add gene plot to an LDheatmap object.

In LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

Add gene plot to an LDheatmap object.

Description

Retrieve genes from the UCSC Genome Browser, generate the genes plot and add it to an LDheatmap object.

Usage

LDheatmap.addGenes(LDheatmap, chromosome, genome = NULL, genesLocation = 0.02,
splice_variants = TRUE, non_coding = TRUE)

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.
genesLocation	The gene plot distance from the LD heat map gene map.
splice_variants	If FALSE, exclude gene splice variants.
non_coding	If FALSE, exclude non-coding genes.

Details

Note: The LDheatmap object should have a non-NULL genetic.distances component. Otherwise the gene map will not be placed correctly. The genes are color coded as follows: black – feature has a corresponding entry in the Protein Data Bank (PDB); dark blue – transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff; medium blue – other RefSeq transcripts; and light blue – non-RefSeq transcripts.

For assemblies older than hg18, all genes are plotted in grey.

Value

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

Author(s)

Sigal Blay <[e-mail]>

References

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

See Also

LDheatmap, plotGenes

Examples

data(GIMAP5.CEU)
ll<-LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position,flip=TRUE)
# Add gene plot
llplusgenes <- LDheatmap.addGenes(ll, chr="chr7", genome="hg18")

LDheatmap documentation built on April 24, 2022, 1:05 a.m.