Create db with decoys and contaminants

Source: R/createDecoyDB.R

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

createDecoyDB(
  dbs,
  useContaminants = loadContaminantsFasta2021(),
  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_contaminants2021_20210929.fasta.gz",package="prozor")
cont <- loadContaminantsFasta2021()
rabbit <-readPeptideFasta(file)
tmp <- 2*(2*length(rabbit)+length(cont)) + 1

res <- createDecoyDB(c(file,file))
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
length(res)
#> [1] 2995
stopifnot(length(res) == tmp)

res <- createDecoyDB(c(file,file), revLab=NULL)
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
stopifnot(length(res) == (2*length(rabbit)+length(cont) + 1))
res <- createDecoyDB(c(file,file), revLab=NULL, useContaminants = NULL)
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
#> reading db :C:/Users/wolski/R/win-library/4.1/prozor/extdata/fgcz_contaminants2021_20210929.fasta.gz
stopifnot(length(res) == (2*length(rabbit) + 1) )