codonSumsPerGroup {ORFik}R Documentation

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 or GRanges object of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in 'reads'

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


[Package ORFik version 1.14.7 Index]