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

In ChromHeatMap: Heat map plotting by genome coordinate

Description

Creates a GRangesList 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 GRangesList on the UCSC browser or not.
session	An optional rtracklayer UCSCSession object. Ignored unless plot=TRUE.

Details

This function is used to create GRangesList 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.

Value

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

Author(s)

Tim F Rayner

References

rtracklayer package

See Also

makeChrStrandData, GRangesList plotChrMap,

Examples

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

ChromHeatMap documentation built on Nov. 8, 2020, 7:33 p.m.