xcombr_db: Generate all combinations of crosslinked peptides

In wfondrie/xcombr: Identifing crosslinked peptides with standard search engines.

Description

Take peptide sequences from one or multiple proteins and generates linearized versions of the potential crosslinked peptides according to the xComb strategy described by Panchaud et al, 2010.

Usage

xcombr_db(x, ...)

## S4 method for signature 'AAString'
xcombr_db(x, xlSpecificity = "Amine:Amine",
  linkType = "both", minLength = 6, maxLength = 24,
  peptideTerminalLink = FALSE, proteinTerminalLink = TRUE,
  customSpecificity = NULL, digest = T, ..., max50 = TRUE)

## S4 method for signature 'AAStringSet'
xcombr_db(x, xlSpecificity = "Amine:Amine",
  linkType = "both", minLength = 6, maxLength = 24,
  peptideTerminalLink = FALSE, proteinTerminalLink = TRUE,
  cleavageRanges = NULL, customSpecificity = NULL, digest = T, ...,
  max50 = TRUE)

Arguments

x	An AAStringSet or AAString
...	Arguments passed to cleave to indicate digestion settings.
xlSpecificity	Defines the crosslinker specificity. Case insensitive.
linkType	Should intra and/or inter-protein crosslinks be considered? Must be either "intra", "inter", or "both"
minLength	Minimum peptide length for either of the crosslinked peptides.
maxLength	Maximum peptide length for either of the crosslinked peptides.
peptideTerminalLink	Should crosslinks at terminal residues of peptides be considered?
proteinTerminalLink	Should crosslinks at terminal residues of the proteins be considered?
customSpecificity	Optional. Used if xlSpecificity = "custom". Must be a character vector of length 2 containing regular expressions for specificity rules.
digest	Locgical indicating the whether the input AAStringSet or AAString should be digested using cleave.
max50	Limits the maximum number of proteins to 50.

wfondrie/xcombr documentation built on May 7, 2019, 9:34 a.m.