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 1.24.2 Index]