R: plot tracks based on gene name

viewGene {trackViewer}

R Documentation

plot tracks based on gene name

Description

given a gene name, plot the tracks.

Usage

viewGene(symbol, filenames, format, txdb, org, upstream = 1000,
  downstream = 1000, anchor = c("gene", "TSS"), plot = FALSE)

Arguments

`symbol`	Gene symbol
`filenames`	files used to generate tracks
`format`	file format used to generate tracks
`txdb`	txdb will be used to extract the genes
`org`	org package name
`upstream`	upstream from anchor
`downstream`	downstream from anchor
`anchor`	TSS, or gene
`plot`	plot the tracks or not.

Value

an invisible list of a trackList, a trackViewerStyle and a GRanges

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
filename = file.path(extdata, "fox2.bed")
optSty <- viewGene("HSPA8", filenames=filename, format="BED", 
                   txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, 
                   org="org.Hs.eg.db")

[Package trackViewer version 1.16.1 Index]