viewGene {trackViewer} | R Documentation |
given a gene name, plot the tracks.
viewGene(symbol, filenames, format, txdb, org, upstream = 1000, downstream = 1000, anchor = c("gene", "TSS"), plot = FALSE)
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. |
an invisible list of a trackList
,
a trackViewerStyle
and a GRanges
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")