createChrMatrix: Generate chromosome-based subset matrices from the mapped...

In ChromHeatMap: Heat map plotting by genome coordinate

Description

Given a data object from makeChrStrandData, generate a matrix containing a subset of the data from a given region of a given chromosome strand, with data binned at appropriate intervals along the chromosome. The minimum width of the binning interval is controlled using the "interval" argument, which can therefore be used to control the output resolution of the data.

Usage

createChrMatrix(data, chr, strand = c('forward','reverse','both'), subset = NULL,
                start=1, end, interval=ceiling((end - start)/500))

Arguments

data	A ChrStrandData object (e.g. generated by makeChrStrandData).
chr	The name of the chromosome to plot.
strand	The chromosome strand to plot (‘both’ indicates that both strands should be overlaid in a single heatmap).
subset	An optional numeric vector indicating which samples should be plotted.
start	The starting chromosome coordinate from which to plot.
end	The ending chromosome coordinate.
interval	The (optional) size of the data bins to use along the chromosome, in bases.

Details

Typically this function will not be called directly, but rather via the wrapper plotChrMap function.

Note that this function may combine data from multiple probes or genes (taking the mean) into a single chromosomal locus based on the size of the specified interval. If this happens the combined probe/gene identifiers are concatenated in the output object, separated by a semicolon.

Value

A ChrStrandMatrix object suitable for use with chrHeatMap and drawMapDendro.

Author(s)

Tim F Rayner

See Also

plotChrMap, chrHeatMap, drawMapDendro, ChrStrandMatrix-class, ChrStrandData-class

Examples

data('demo')
stranddata <- createChrMatrix( chrdata, chr=22, strand='forward', start=21925000, end=24300000 )

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