coveragePerTiling {ORFik} | R Documentation |
It tiles each GRangesList group to width 1, and finds hits per position. A range from 1:5 will split into c(1,2,3,4,5) and count hits on each.
coveragePerTiling( grl, reads, is.sorted = FALSE, keep.names = TRUE, as.data.table = FALSE, withFrames = FALSE )
grl |
a |
reads |
a GAlignment or GRanges object of RiboSeq, RnaSeq etc. |
is.sorted |
logical (F), is grl sorted. |
keep.names |
logical (T), keep names or not. |
as.data.table |
a logical (FALSE), return as data.table with 2 columns, position and count. |
withFrames |
a logical (FALSE), only available if as.data.table is TRUE, return the ORF frame, 1,2,3, where position 1 is 1, 2 is 2 and 4 is 1 etc. |
This is a safer speedup of coverageByTranscript from GenomicFeatures. It also gives the possibility to return as data.table, for faster computations. NOTE: If reads contains a $score column, it will presume that this is the number of replicates per reads, weights for the coverage() function. So delete the score column if this is wrong.
a RleList, one integer-Rle per group with # of hits per position. Or data.table if as.data.table is TRUE.
Other ExtendGenomicRanges:
asTX()
,
overlapsToCoverage()
,
reduceKeepAttr()
,
tile1()
,
txSeqsFromFa()
,
windowPerGroup()
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)), strand = "+") grl <- GRangesList(tx1_1 = ORF) RFP <- GRanges("1", IRanges(25, 25), "+") coveragePerTiling(grl, RFP, is.sorted = TRUE) # now as data.table with frames coveragePerTiling(grl, RFP, is.sorted = TRUE, as.data.table = TRUE, withFrames = TRUE)