contiBAIT: contiBAIT - master function to process strand-seq libraries...

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

Description

contiBAIT – master function to process strand-seq libraries into ordered linkage groups

Usage

contiBAIT(path = ".", cluster = 1, clusterParam = NULL,
  saveName = FALSE, filter = FALSE, readQual = 10, readLimit = 10,
  pairedEnd = TRUE, makePlots = FALSE, verbose = TRUE)

Arguments

path	String denoting location of Strand-seq bam files (default is ".")
cluster	Integer denoting the number of reclusterings to be performed for creating linkage groups (default is 1)
clusterParam	Number of parallel processors to use when clustering contigs. Default is NULL.
saveName	String denoting the file name for saved data. If FALSE, no intermediate files are saved (default is FALSE)
filter	additional file to split chromosomes based on locations. If this parameter is blank, a filter table will be automatically generated from the header of the first file in bamFileList
readQual	Integer dictating the minimal mapping quality required for a read to be accepted. Default is 10.
readLimit	Minimum number of reads on a contig to make a strand call. 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
makePlots	Logical determining whether plots should be created. Default is TRUE
verbose	prints messages to the terminal (default is TRUE)

Value

ordered contigs in bed format. Depending on options, intermediate files and plots will also be generated

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")
library(BiocParallel)

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

orderedContigs <- contiBAIT(path=example.dir, 
							cluster=1, 
							clusterParam=MulticoreParam(), 
							filter=exampleDividedChr, 
							pairedEnd=FALSE)

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