BAIT: BAIT - master function to process strand-seq libraries into...

In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

BAIT – master function to process strand-seq libraries into BAIT ideograms

Usage

BAIT(path = ".", splitBy = 2e+05, readQual = 10, pairedEnd = TRUE,
  plotBy = "lib", plotName = NULL, chroms = "all", verbose = TRUE)

Arguments

path	String denoting location of Strand-seq bam files (default is ".")
splitBy	numeric value of binsize for plotting. default is 200000
readQual	Integer dictating the minimal mapping quality required for a read to be accepted. Default is 10.
pairedEnd	Whether the bam files being read are in paired end format. Default is TRUE. Note,
plotBy	Whether to plot by library ('lib') or chromosome ('chr')
plotName	character which determines file name to be saved. Default is to open an R plot from the terminal
chroms	vector of chromosome number to prevent contig plotting. eg for humans use 1:24. Default is 'all'
verbose	prints messages to the terminal (default is TRUE)

Value

ideogram plots

Examples

## Not run: 

#Not run because this takes a minute or two:
bamPath=file.path(system.file(package='contiBAIT'), 'extdata')

BAIT(bamPath, pairedEnd = FALSE) #our example data is single-end

## End(Not run)

contiBAIT documentation built on Nov. 8, 2020, 5:49 p.m.