contiBAIT (version 1.0.0)

StrandFreqMatrix-class: A class for storing a matrix of frequencies of Watson to Crick reads for a set of contigs over several libraries

Description

The strand information stored in this object is the ratio of Watson to Crick reads mapping to each contig in each library (cell). This should fall within the range (-1,1). This class simply extends matrix, but with additional validity checking.

Constructor for StrandFreqMatrix

Usage

StrandFreqMatrix(counts = matrix(double()))

Arguments

counts

a double matrix of read count ratios

Value

• a StrandFreqMatrix

Examples

data("exampleWatsonFreq")
data("exampleCrickFreq")
frequencyMatrix <- sapply(1:ncol(exampleCrickFreq), 
function(colNum){exampleCrickFreq[,colNum] / exampleWatsonFreq[,colNum]})

StrandFreqMatrix(frequencyMatrix)