coveragePerTiling {ORFik}R Documentation

Get coverage per group

Description

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.

Usage

coveragePerTiling(
  grl,
  reads,
  is.sorted = FALSE,
  keep.names = TRUE,
  as.data.table = FALSE,
  withFrames = FALSE
)

Arguments

grl

a GRangesList of 5' utrs or transcripts.

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.

Details

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.

Value

a RleList, one integer-Rle per group with # of hits per position. Or data.table if as.data.table is TRUE.

See Also

Other ExtendGenomicRanges: asTX(), overlapsToCoverage(), reduceKeepAttr(), tile1(), txSeqsFromFa(), windowPerGroup()

Examples

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)


[Package ORFik version 1.6.9 Index]