interestGenes_ENSEMBL: Create one track of the genes in the genomic regions of...

In TiphaineCMartin/coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Create one track of the genes in the genomic regions of interest from EMSEMBL

Description

Create one track of the genes in the genomic regions of interest from EMSEMBL using the Gviz bioconductor package

Usage

interestGenes_ENSEMBL(gen, chr, start, end, interestfeatures,interestcolor,
showId=FALSE,title="genes (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, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr15"
start <- 75011669
end <- 75019876
interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good"))
interestcolor <- list("bad"="red", "good"="green")

if(interactive()) {
  interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,
  interestfeatures,interestcolor,showId=TRUE)
  plotTracks(interestgenesENSMBLtrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(interestgenesENSMBLtrack)
  plotTracks(interestgenesENSMBLtrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.