annotate.protein_id {specL} | R Documentation

## Annotate protein_id

### Description

This function assigns the protein identifier for a list of tandem mass specs having a peptide sequence assigned.

### Usage

    annotate.protein_id(data, file = NULL, fasta = read.fasta(file = file,
             as.string = TRUE, seqtype = "AA"), digestPattern = "(([RK])|(^)|(^M))")

### Arguments

`data` | list of records containing mZ and peptide sequences.
`file` | file name of a FASTA file.
`fasta` | a fasta object as returned by the `seqinr::read.fasta(...)` method.
`digestPattern` | a regex pattern which can be used by the `grep` command. the default regex pattern assumes a tryptic digest.

### Details

The protein sequences a read by the `read.fasta` function of the `seqinr` package. The protein identifier is written to the protein `proteinInformation` variable.

If the function is called on a multi-core architecture it uses `mclapply`.

It is recommended to load the FASTA file prior to running `annotate.protein_id` using

`myFASTA <- read.fasta(file = file, as.string = TRUE, seqtype = "AA")`

instead of providing the FASTA file name to the function.

### Value

it returns a list object.

### Author(s)

Jonas Grossmann and Christian Panse, 2014

### See Also

`?read.fasta` of the `seqinr` package.

http://www.uniprot.org/help/fasta-headers

### Examples

        # annotate.protein_id

        # our Fasta sequence
          irtFASTAseq <- paste(">zz|ZZ_FGCZCont0260|",
          "iRT_Protein_with_AAAAK_spacers concatenated Biognosys\n",
          "LGGNEQVTRAAAAKGAGSSEPVTGLDAKAAAAKVEATFGVDESNAKAAAAKYILAGVENS",
          "KAAAAKTPVISGGPYEYRAAAAKTPVITGAPYEYRAAAAKDGLDAASYYAPVRAAAAKAD",
          "VTPADFSEWSKAAAAKGTFIIDPGGVIRAAAAKGTFIIDPAAVIRAAAAKLFLQFGAQGS",
          "PFLK\n")

        # be realistic, do it from file
          Tfile <- file();  cat(irtFASTAseq, file = Tfile);

        #use read.fasta from seqinr
          fasta.irtFASTAseq <-read.fasta(Tfile, as.string=TRUE, seqtype="AA")
          close(Tfile)

        #annotate with proteinID
        # -> here we find all psms from the one proteinID above
          peptideStd <- specL::annotate.protein_id(peptideStd,
          fasta=fasta.irtFASTAseq)

        #show indices for all PSMs where we have a proteinInformation
         which(unlist(lapply(peptideStd,
          function(x){nchar(x$proteinInformation)>0})))

[Package specL version 1.21.2 Index]