createDecoyDB: Create db with decoys and contaminants

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

Create db with decoys and contaminants

Description

For more details and references see package vignette vignette("CreateDecoyDB", package = "prozor")

Usage

createDecoyDB(
  dbs,
  useContaminants = loadContaminantsFGCZ2022(),
  revLab = "REV_",
  annot = "zz|sourceOf|database"
)

Arguments

dbs	a path to a fasta file or an array of files
useContaminants	list with contaminant sequences
revLab	label for reversed peptides (if NULL do not generate decoys)
annot	source of database

Value

list of SeqFastaAA entries

Examples

file = system.file("extdata/fgcz_contaminants2022_20220405.fasta.gz",package="prozor")
cont <- loadContaminantsFGCZ2022()
rabbit <-readPeptideFasta(file)
tmp <- 2*(2*length(rabbit)+length(cont)) + 1
res <- createDecoyDB(c(file,file))
length(res)
stopifnot(length(res) == tmp)

res <- createDecoyDB(c(file,file), revLab=NULL)
stopifnot(length(res) == (2*length(rabbit)+length(cont) + 1))
res <- createDecoyDB(c(file,file), revLab=NULL, useContaminants = NULL)
stopifnot(length(res) == (2*length(rabbit) + 1) )

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