contiBAIT (version 1.0.0)

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

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 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