artificial.orfs: Create small artificial orfs from cds

In Roleren/ORFik: Open Reading Frames in Genomics

Create small artificial orfs from cds

Description

Usefull to see if short ORFs prediction is dependent on length.
Split cds first in two, a start part and stop part. Then say how large the two parts can be and merge them together. It will sample a value in range give.
Parts will be forced to not overlap and can not extend outside original cds

Usage

artificial.orfs(
  cds,
  start5 = 1,
  end5 = 4,
  start3 = -4,
  end3 = 0,
  bin.if.few = TRUE
)

Arguments

cds	a GRangesList of orfs, must have width %% 3 == 0 and length >= 6
start5	integer, default: 1 (start of orf)
end5	integer, default: 4 (max 4 codons from start codon)
start3	integer, default -4 (max 4 codons from stop codon)
end3	integer, default: 0 (end of orf)
bin.if.few	logical, default TRUE, instead of per codon, do per 2, 3, 4 codons if you have few samples compared to lengths wanted, If you have 4 cds' and you want 7 different lengths, which is the standard, it will give you possible nt length: 6-12-18-24 instead of original 6-9-12-15-18-21-24. If you have more than 30x cds than lengths wanted this is skipped. (for default arguments this is: 7*30 = 210 cds)

Details

If artificial cds length is not divisible by 2, like 3 codons, the second codon will always be from the start region etc.
Also If there are many very short original cds, the distribution will be skewed towards more smaller artificial cds.

Value

GRangesList of new ORFs (sorted: + strand increasing start, - strand decreasing start)

Examples

txdb <- ORFik.template.experiment()
#cds <- loadRegion(txdb, "cds")
## To get enough CDSs, just replicate them
# cds <- rep(cds, 100)
#artificial.orfs(cds)

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.