plot tracks based on gene name

given a gene name, plot the tracks.

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")
#>   403 genes were dropped because they have exons located on both strands
#>   of the same reference sequence or on more than one reference sequence,
#>   so cannot be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a
#>   GRangesList object, or use suppressMessages() to suppress this message.