refGenes_UCSC: Create a track of RefSeq genes from the UCSC genome browser

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

View source: R/BiofeatureGraphics.R

Description

Create a track of RefSeq genes from the UCSC genome browser using the Gviz bioconductor package

Usage

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refGenes_UCSC(gen, chr, start, end, title="Ref Genes UCSC", track = "refGene",
IdType="Ref", showId=TRUE)

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

track

the name of table in UCSC for the group "Genes and Gene Prediction"

IdType

When set to 'ref' shows the gene reference, when set to "name" shows the gene name

showId

Shows the ID or name of the genetic elements

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=knownGene

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

See Also

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

Examples

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library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38203219
end <- 38303219
IdType <- "name"
track <- "refGene"

if(interactive()) {
  genesUcsctrack<-refGenes_UCSC(gen,chr,start,end,track,IdType)
  plotTracks(genesUcsctrack, from = start, to =end)
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, from = start, to =end)
}

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