View source: R/LDheatmap.addGenes.R
LDheatmap.addGenes | R Documentation |
Retrieve genes from the UCSC Genome Browser, generate the genes plot and add it to an LDheatmap object.
LDheatmap.addGenes(LDheatmap, chromosome, genome = NULL, genesLocation = 0.02, splice_variants = TRUE, non_coding = TRUE)
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 |
non_coding |
If |
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.
An object of class LDheatmap given as an argument, with the grob
LDheatmapGrob
modified to inclue the "transcripts"
child grob.
Sigal Blay <sblay@sfu.ca>
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene
LDheatmap
, plotGenes
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")
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