Numeric distributions by nucleotide - class

Description

An S4 class that inherits from eSet and holds all the numeric distributions of functions defined over the genome. The values may include coverage, splicing, fold change, etc. for a region defined by genomic coordinates.

Slots/List Components

Objects of this class contain (at least) the following list components:

chr: numeric matrix containing the read counts.

start: data.frame containing the library size and group labels.

end: data.frame containing the library size and group labels.

strand: data.frame containing the library size and group labels.

start: data.frame containing the library size and group labels.

Methods

distribs gives the matrix of distributions from assayData

getDistr gives a single distributions from assayData as a vector

newNuctleotideDistr (distribs, chr, start, end, strand, type="UNKNOWN", phenoData=NULL, featureData=NULL) constructor from a matrix of data and chromosome coordinates.

Author(s)

Anna Lesniewska, Michal Okoniewski

See Also

SeqReads, NDtransforms