collapseDuplicatedReads,GAlignments-method {ORFik} | R Documentation |
For every GRanges, GAlignments read, with the same: seqname, start, (cigar) / width and strand, collapse and give a new meta column called "score", which contains the number of duplicates of that read. If score column already exists, will return input object!
## S4 method for signature 'GAlignments' collapseDuplicatedReads(x, addScoreColumn = TRUE, reuse.score.column = TRUE)
x |
a GRanges, GAlignments or GAlignmentPairs object |
addScoreColumn |
= TRUE, if FALSE, only collapse and not keep score column of counts for collapsed reads. Returns directly without collapsing if reuse.score.column is FALSE and score is already defined. |
reuse.score.column |
logical (TRUE), if addScoreColumn is TRUE, and a score column exists, will sum up the scores to create a new score. If FALSE, will skip old score column and create new according to number of replicated reads after conversion. If addScoreColumn is FALSE, this argument is ignored. |
a GRanges, GAlignments or GAlignmentPairs object, same as input
gr <- rep(GRanges("chr1", 1:10,"+"), 2) collapseDuplicatedReads(gr)