ChrStrandData: Class to contain data associated with chromosome coordinates across a whole genome.

Description

Container for data from high-throughput assays mapped to chromosome locations.

Arguments

Creating Objects

The most convenient way to create a ChrStrandData object is to use the makeChrStrandData function, which can be used to convert data stored in either an ExpressionSet or data frame into a ChrStrandData object: makeChrStrandData(ALL, lib = "hgu95av2.db")

Slots

data: a 'list', whose components correspond to samples in the same order as appearing in the columns of 'expr'. Each component is also a 'list', named by chromosomes "1"-"22", "X" and "Y". Each named component is again a 'list' with two elements named "posS" and "negS", corresponding to the forward and reverse strands of a chromosome, each of which is a list containing start coordinates ("x"), end coordinates("xe") and the corresponding data values ("y").
lib: A string giving the name of the annotation data package to use.
chrs: The list of chromosomes represented in the object.

Methods

Class-specific methods.

annotation(ChrStrandData): Returns the name of the AnnotationDbi library used to annotate the object.
chrNames(ChrStrandData): Returns a list of the chromosomes represented in the object.
sampleNames(ChrStrandData): Returns the names of the samples associated with the object.

Standard generic methods:

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

Examples

Run this code

data('demo')
chrdata <- makeChrStrandData(exprs(ALLs.chr22), lib = "hgu95av2.db")