StrandFreqMatrix-class {contiBAIT} | R Documentation

## 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.

### 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)

[Package contiBAIT version 1.20.0 Index]