ChrStrandMatrix-class: Class to contain data associated with genome locations for a...
In ChromHeatMap: Heat map plotting by genome coordinate

Description Creating Objects Slots Methods Author(s) See Also Examples

Container for chromosome-specific subsets of data selected from an genome-wide ChrStrandData object, suitable for use with chrHeatMap.

Typically, objects of this class are created and used internally by the createChrMatrix and chrHeatMap functions. Objects can be created in a similar fashion by end-users:

createChrMatrix(chrdata, chr=22, strand='forward', start=21925000, end=24300000, interval=5000)

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.

data: The data matrix, arranged with samples in columns and genomic locations in rows.
probeID: An array of probe or gene identifiers associated with the data. The names attached to this array correspond with chromosome coordinate (specifically, the starting coordinates, i.e. the left-hand edges). These identifiers will ultimately be returned by e.g. the grabChrMapProbes function.
chr: The chromosome name or number.
strand: The chromosome strand ('forward', 'reverse' or 'both').
start: The starting chromosome coordinates for each genomic location.
end: The ending chromosome coordinates for each genomic location.

Class-specific methods.

chrNames(ChrStrandMatrix): Returns the name of the chromosome for the object.
strandName(ChrStrandMatrix): Returns the chromosome strand for the object.
sampleNames(ChrStrandMatrix): Returns the names of the samples associated with the object.
featureNames(ChrStrandMatrix): Returns the probe or gene identifiers associated with the object.
exprs(ChrStrandMatrix): Returns the chromosome-specific data matrix for the object.

Standard generic methods:

show(ChrStrandMatrix): Generates a short description of the ChrStrandMatrix object.
summary(ChrStrandMatrix): Generates a summary of the data available for each sample in the ChrStrandMatrix object.

Tim F Rayner

createChrMatrix, ChrStrandData-class.