codonSumsPerGroup: Get read hits per codon
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Details Value

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

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

`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)

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.

a data.table with codon sums

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