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]