thoroughBed: thoroughBed - function to merge chromosomes from libraries...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

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

Usage

## S4 method for signature 'ANY,LibraryGroupList'
thoroughBed(bamFileList, relatedLibList,
  qual = 10, pairedEnd = TRUE, rmdup = 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
rmdup	Logical as to whether to remove duplicate reads within each library. Default is TRUE.
verbose	prints messages to the terminal (default is TRUE)

Value

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

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("exampleLibList")


library(BiocParallel)

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

exampleRange <- thoroughBed(example.dir, exampleLibList)

show(exampleRange)

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.