createUniquePeptideDbRds: Create an RDS file for the 'Unique Peptides Database'

In synapter: Label-free data analysis pipeline for optimal identification and quantitation

Description

This function creates an RDS file to store the “Unique Peptides Database” for future runs of synergise or Synapter.

Usage

createUniquePeptideDbRds(fastaFile, outputFile = paste0(fastaFile, ".rds"),
  missedCleavages = 0, IisL = FALSE, verbose = interactive())

Arguments

fastaFile	file path of the input fasta file
outputFile	file path of the target RDS file; must have the file extension ".rds"
missedCleavages	Number of maximal allowed missed cleavages. Default is 0.
IisL	If TRUE Isoleucin and Leucin are treated as identical. In this case sequences like "ABCI", "ABCL" are removed because they are not unqiue. If FALSE (default) "ABCI" and "ABCL" are reported as unique.
verbose	If TRUE a verbose output is provied.

Author(s)

Sebastian Gibb <[e-mail]>

See Also

Synapter for details about the cleavage procedure.

Examples

## Not run: 
createUniquePeptideDbRds("uniprot.fasta", "uniprot.fasta.rds")

## End(Not run)

synapter documentation built on Nov. 8, 2020, 6:25 p.m.