thoroughBed – function to merge chromosomes from libraries that have the same strand states

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Description

thoroughBed – function to merge chromosomes from libraries that have the same strand states

Usage

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## S4 method for signature 'ANY,LibraryGroupList'
thoroughBed(bamFileList, relatedLibList,
  qual = 10, pairedEnd = TRUE, verbose = TRUE)

Arguments

bamFileList

vector containing the location of the bams file to be read

relatedLibList

list where each element contains all library names that show similar strand pattern. The product of findSimilarLibraries

qual

Mapping quality threshold. Default is 10

pairedEnd

Whether the bam files being read are in paired end format. Default is TRUE. Note, since paired reads will be the same direction, only first mate read of pair is used in output to reduce file size

verbose

prints messages to the terminal (default is TRUE)

Value

a GRanges object comprising merged directional reads from all libraries in relatedLibList.

Examples

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#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("exampleLibList")


library(BiocParallel)

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

exampleRange <- thoroughBed(example.dir, exampleLibList)

show(exampleRange)

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