viewGene: plot tracks based on gene name

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

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")

jianhong/trackViewer documentation built on March 17, 2024, 2:16 p.m.