findSimilarLibraries,StrandStateMatrix,StrandReadMatrix,ChrTable-method {contiBAIT} | R Documentation

## findSimilarLibraries – function to identify libraries that hare similar WC patterns on chromosomes

### Description

findSimilarLibraries – function to identify libraries that hare similar WC patterns on chromosomes

### Usage

      ## S4 method for signature 'StrandStateMatrix,StrandReadMatrix,ChrTable'
    findSimilarLibraries(strandStateMatrix,
      strandReadMatrix, chrGrange, chrNum, cluster = 1, clusterParam = NULL,
      verbose = TRUE)

### Arguments

`strandStateMatrix` | A strandStateMatrix object for all libraries across split fragments, derived from preprocessStrandTable
`strandReadMatrix` | The number of reads present for each strandStateMatrix element. An object of type strandReadMatrix from strandSeqFreqTable
`chrGrange` | File of type ChrTable (a GRanges object with a meta column titled 'name' determining contig name) to split chromosomes based on locations. name meta should match the rownames of strandStateMatrix and strandReadMatrix
`chrNum` | The chromosome number to analyse
`cluster` | Number of times to recluster and take the consensus of. If NULL, clustering is run only once
`clusterParam` | optional `BiocParallelParam` specifying cluster to use for parallel execution. When `NULL`, execution will be serial.
`verbose` | prints messages to the terminal (default is TRUE)

### Value

a list of type LinkageGroupList with two elements; libraries that are mostly Watson, and those that are mostly Crick

### Examples

    #Get a list of BAM files containing libraries for cells from the same organism, aligned to the same genome
    #In this case these are the example BAM files provided with the package (hence the call to system.file);
    data("exampleDividedChr")
    data("exampleWCMatrix")
    data("exampleReadCounts")

    library(BiocParallel)

    example.dir <- file.path(system.file(package='contiBAIT'), 'extdata')

    chrGrange <- exampleDividedChr[which(exampleDividedChr$name %in% rownames(exampleWCMatrix))]

    exampleLibList <- lapply(seq_len(length(unique(seqnames(chrGrange)))), function(x) findSimilarLibraries(exampleWCMatrix, exampleReadCounts, chrGrange, x, cluster=1, clusterParam=MulticoreParam()))
    exampleLibList <- exampleLibList[!sapply(exampleLibList, is.null)]
    exampleLibList <- LibraryGroupList(exampleLibList)

    show(exampleLibList)

[Package contiBAIT version 1.15.0 Index]