locateMisorients: locateMisorients - function to identify libraries that hare...

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

Description

locateMisorients – function to identify libraries that hare similar WC patterns on chromosomes

Usage

## S4 method for signature 'GRanges'
locateMisorients(compiledGrange, gapFile = NULL,
  stateNum = 3, readCutOff = 40, verbose = TRUE)

Arguments

compiledGrange	A GRanges object consisting of read locations. Can be an individual file or the product of thoroughBed
gapFile	A GRanges object consisting of start and end locations of assembly gaps (defaul it NULL)
stateNum	The number of expected strand states. Default is 3 (WW, WC and CC). Function may exhibit unusual behaviour is changed
readCutOff	The minimal number of reads required to make an accurate strand state call. Default is 40.
verbose	prints messages to the terminal (default is TRUE)

Value

a list of ChrTable objects. The first is a ChrTable of misorientations detected. The second is a ChrTable of chimera detected. Output can be used in downstream functions (strandSeqFreqTable)

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