findconsensusRegions {soGGi} | R Documentation |
Plot coverage of points or regions.
Returns summits and summmit scores after optional fragment length prediction and read extension
findconsensusRegions(testRanges, bamFiles = NULL, method = "majority", summit = "mean", resizepeak = "asw", overlap = "any", fragmentLength = NULL, NonPrimaryPeaks = list(withinsample = "drop", betweensample = "mean")) summitPipeline(reads, peakfile, fragmentLength, readlength)
testRanges |
Named character vector of region locations |
bamFiles |
Named character vector of bamFile locations |
method |
Method to select reproducible summits to merge. |
summit |
Only mean avaialble |
resizepeak |
Only asw available |
overlap |
Type of overlap to consider for finding consensus sites |
fragmentLength |
Predicted fragment length. Set to NULL to auto-calculate |
NonPrimaryPeaks |
A list of parameters to deal with non primary peaks in consensus regions. |
peakfile |
GRanges of genomic intervals to summit. |
reads |
Character vector of bamFile location or GAlignments object |
readlength |
Read length of alignments. |
Consensus A GRanges object of consensus regions with consensus summits.
Summits A GRanges object of summits and summit scores.