codonSumsPerGroup: Get read hits per codon

In Roleren/ORFik: Open Reading Frames in Genomics

Get read hits per codon

Description

Helper for entropy function, normally not used directly Seperate each group into tuples (abstract codons) Gives sum for each tuple within each group

Usage

codonSumsPerGroup(grl, reads, weight = "score", is.sorted = FALSE)

Arguments

grl	a GRangesList of 5' utrs, CDS, transcripts, etc.
reads	a GAlignments, GRanges, or precomputed coverage as covRle (one for each strand) of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in 'reads'. Can also be random access paths to bigWig or fstwig file. Do not use random access for more than a few genes, then loading the entire files is usually better. File streaming is still in beta, so use with care!
weight	(default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik ofst, bedoc and .bedo files contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually.
is.sorted	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)

Details

Example: counts c(1,0,0,1), with reg_len = 2, gives c(1,0) and c(0,1), these are summed and returned as data.table 10 bases, will give 3 codons, 1 base codons does not exist.

Value

a data.table with codon sums

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