reverseSeq: create rev sequences to fasta list

In protViz/prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

create rev sequences to fasta list

Description

peptides which do not have protein assignment drop out

Usage

reverseSeq(fasta, revLab = "REV_")

Arguments

fasta	- an r list with SeqFastaAA
revLab	- how to label reverse sequences, default = REV_

Value

string with reversed sequence

Examples

library(seqinr)
#library(prozor)

file = system.file("extdata/fgcz_contaminants2021_20210929.fasta.gz", package="prozor")
fasta = readPeptideFasta(file = file)
getAnnot(fasta[[1]])
x <- reverseSeq(fasta)

revseq <- reverseSeq(fasta ,revLab = "REV_")
stopifnot(length(revseq) == length(fasta))
stopifnot(grep("^REV_","REV_zz|ZZ_FGCZCont0000|")==1)

tmp <- list(as.SeqFastaAA(("DYKDDDDK"),name="Flag|FLAG|p2079",Annot=""))

reverseSeq(tmp)

protViz/prozor documentation built on Oct. 17, 2023, 6:39 p.m.