coverageByTranscriptW: coverageByTranscript with weights

In JokingHero/ORFik: Open Reading Frames in Genomics

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

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.