locateMisorients: locateMisorients - function to identify libraries that hare...
In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

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

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

`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)

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)

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