xenorefGenes_UCSC: Create a track for xeno-reference genes from the UCSC genome...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

Description

Create a track for xeno-reference genes from the UCSC genome browser using the Gviz bioconductor package

Usage

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xenorefGenes_UCSC(gen, chr, start, end,title="Other RefSeq", showId=FALSE)

Arguments

gen

the name of the genome

chr

the chromosome of interest

start

the first position in the region of interest (the smallest value)

end

the last position in the region of interest (the largest value)

title

Name of tracks

showId

Show the ID of the genetic elements

Value

A UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL,transcript_ENSEMBL,

Examples

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library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()){
  xenogenestrack<-xenorefGenes_UCSC(gen,chr,start,end,showId=TRUE)
  plotTracks(xenogenestrack, from=start, to=end)
} else {
  data(xenogenestrack)
  plotTracks(xenogenestrack, from=start, to=end)
}

coMET documentation built on Nov. 1, 2018, 2:17 a.m.