getallseq: getallseq

In mgerault/DIAgui: A shiny app for processing DIAnn output in proteomics

getallseq

Description

Get theoretical peptide sequence from proteins (from data bank or fasta files), thanks to seqinr package.

Usage

getallseq(
  spec = "Saccharomyces cerevisiae",
  pr_id = "P09938",
  bank_name = "swissprot",
  fasta_file = FALSE,
  verbose = TRUE
)

Arguments

spec	The species name corresponding to the proteins from pr_id.
pr_id	The proteins that you want to get the theoretical peptide sequence from.
bank_name	The name of the data bank you want to use to get theoretical peptide. If you want to use you're own fasta files, you can put the path (or several in a double) to your fasta files and set fasta_file to TRUE.
fasta_file	Logical to tell if you use fasta file in bank_name.
verbose	Logical to tell if you want to print advancement.

Details

Charif D, Lobry J (2007). “SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.” In Bastolla U, Porto M, Roman H, Vendruscolo M (eds.), Structural approaches to sequence evolution: Molecules, networks, populations, series Biological and Medical Physics, Biomedical Engineering, 207-232. Springer Verlag, New York. ISBN : 978-3-540-35305-8.

If the protein is grouped, it will only take the first protein.

Value

A list containing the peptide sequence from each protein.

mgerault/DIAgui documentation built on Nov. 7, 2024, 12:12 a.m.