coverageByTranscriptW: coverageByTranscript with weights

coverageByTranscriptWR Documentation

coverageByTranscript with weights

Description

Extends the function with weights, see coverageByTranscript for original function.

Usage

coverageByTranscriptW(
  x,
  transcripts,
  ignore.strand = FALSE,
  weight = 1L,
  seqinfo.x.is.correct = FALSE
)

Arguments

x

reads (GRanges, GAlignments)

transcripts

GRangesList

ignore.strand

a logical (default: FALSE)

weight

a vector (default: 1L), if single number applies for all, else it must be the string name of a defined meta column in "x", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment was found 5 times.

seqinfo.x.is.correct

logical, default FALSE. If you know x, has correct seqinfo, then you can save some computation time by setting this to TRUE.

Value

Integer Rle of coverage, 1 per transcript


Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.