ChromHeatMap (version 1.26.0)

makeRangedDataList: Plot expression data as tracks in the UCSC genome browser

Description

Creates a RangedDataList object suitable for uploading to the UCSC genome browser using the rtracklayer package.

Usage

makeRangedDataList( data, chr, start = 1, end, genome, subset = NULL, cytoband, plot=FALSE, session )

Arguments

data

A ChrStrandData object, output from the makeChrStrandData function.

chr

Chromosomal id, chromosome to plot 1:22,X,Y.

start

Optional start chromosome position from which to commence plotting.

end

Optional end chromosome position.

genome

The name of the genome from which the data coordinates are taken (e.g. "hg18"). Passed to GenomicData in the rtracklayer package.

subset

Optional numeric vector listing the samples from data to plot.

cytoband

Optional cytological band to plot (e.g. `q23').

plot

An optional flag indicating whether to automatically plot the resulting RangedDataList on the UCSC browser or not.

session

An optional rtracklayer UCSCSession object. Ignored unless plot=TRUE.

Value

A RangedDataList object containing the data for the specified genome region. See the rtracklayer package for more information on this object class.

Details

This function is used to create RangedDataList objects from ChrStrandData objects (see the makeChrStrandData function). If the plot argument is set to TRUE, the data is also uploaded to a UCSC browser session using default settings. See the rtracklayer package for more information on RangedData and UCSCSession objects.

References

rtracklayer package

See Also

makeChrStrandData, RangedDataList plotChrMap,

Examples

data('demo')
r <- makeRangedDataList( data=chrdata, chr=22, cytoband='q11.23', genome='hg18' )