parse.seq: Parse an amino acid sequence into a set of peptides,...

Description Usage Arguments Examples

View source: R/parse_seq.R

Description

Parse an amino acid sequence into a set of peptides, incorporating hydroxylation and deamidation modifications, and calculating mass

Usage

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parse.seq(sequence, cuts = "K|R", skip = "X", massmin = 800,
  massmax = 3500, verbose = F, max.missed.cleaves = 0, cutbefore = F)

Arguments

cuts

a regular expression listing the amino acids that the sequence should be cut at. Defaults to Trypsing cut sites K & R

skip

any codes that mean the peptide is invalid. Defaults to "X"

massmin

the minimum mass that a peptide should be. Defaults to 800

massmax

the maximum mass that a peptide should be. Defaults to 3500

verbose

whether to print messages to console during processing. Defaults to FALSE

max.missed.cleaves

the number of missed cleaves to incorporate in the set of peptides.

seqeunce

a character string holding the sequence, e.g. "GPPGAPGPPGPP"

Examples

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parse.seq("GPPGQKGPPGPQGPRGPPGPPGPM")

bioarch-sjh/bacollite documentation built on Dec. 13, 2018, 10:28 p.m.