locateMisorients,GRanges-method {contiBAIT} | R Documentation

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

### 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)

[Package contiBAIT version 1.15.0 Index]