ChrStrandMatrix: Class to contain data associated with genome locations for a specific chromosome.

Description

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

Arguments

Creating Objects

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.

Slots

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.

Methods

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.

Examples

Run this code

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