codonSumsPerGroup: Get read hits per codon

Description Usage Arguments Details Value

View source: R/feature_helpers.R

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

1
codonSumsPerGroup(grl, reads, weight = "score", is.sorted = FALSE)

Arguments

grl

GRangesList or GRanges of your ranges

reads

GRanges object of your 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 .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


ORFik documentation built on March 27, 2021, 6 p.m.