interestTranscript_ENSEMBL: Create a track of transcripts from ENSEMBL

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

View source: R/BiofeatureGraphics.R

Description

Create a track to visualize different transcripts from ENSEMBL using the Gviz bioconductor package

Usage

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interestTranscript_ENSEMBL(gen, chr, start, end,interestfeatures,
interestcolor,showId = FALSE, title="transcripts ENSEMBL")

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)

interestfeatures

A data frame with 3 columns: start of features, end of features, and type of features

interestcolor

A list with the color for each new features defined

showId

Show the ID of the genetic elements

title

Name of tracks

Value

A BiomartGeneRegionTrack object of Gviz

Author(s)

Tiphaine Martin

References

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

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

See Also

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

Examples

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library("Gviz")
gen <- "hg19"
chr <- "chr15"
start <- 75011669
end <- 75019876
interestfeatures <- rbind(c("75017782","75017835","bad"),c("75013755","75013844","good"))
interestcolor <- list("bad"="red", "good"="green")

if(interactive()){
  interesttransENSMBLtrack<-interestTranscript_ENSEMBL(gen,chr,start,end,
  interestfeatures,interestcolor,showId=TRUE)
  plotTracks(interesttransENSMBLtrack, from=start, to=end)
} else {
  data(interesttransENSMBLtrack)
  plotTracks(interesttransENSMBLtrack, from=start, to=end)
}

coMET documentation built on May 2, 2018, 4:21 a.m.