Description Usage Arguments Value
locateMisorients – function to identify libraries that hare similar WC patterns on chromosomes
1 2 3 | ## 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)
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