countPotModifAAs: Make Table With Counts of Potential Modification Sites

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Make Table With Counts of Potential Modification Sites

Description

Makes table 'cou' with counts of (potential) modification sites based on column 'seq' in matrix 'pepTab'. Note: if multiple N-or C-term modifs, then only the first is shown in resulting table 'cou'.

Usage

countPotModifAAs(
  pepTab,
  modTy,
  maxMod = c(p = 3, h = 1, k = 1, o = 1, m = 1, n = 1, u = 1, r = 1, s = 1),
  specAAMod = NULL,
  knownMods = NULL,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

pepTab	(matrix) peptide sequences, start and end sites, typically result from makeFragments
modTy	(list) modifications : $basMod for character vector of fixed modifications and $varMod for variable modifications. For one letter-code see AAfragSettings("modChem")
maxMod	(integer) maximal number variable modifications will be considered in given fragment (may increase complexity and RAM consumption)
specAAMod	(list) optional custom list showing which AA to be considered with which (one-letter) modification code (default AAfragSettings)
knownMods	(list) optional custom list showing which modification appears at what type of location, eg N-terminal, internal ... (default AAfragSettings)
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of message(s) produced
debug	(logical) for bug-tracking: more/enhanced messages and intermediate objects written in global name-space

Value

list of matrixes $cou and $combTerm, with number of modifications per peptides (line in 'pepTab') for basMod, varMod & varMo2

See Also

AAfragSettings, makeFragments

Examples

protP2 <- c(mesp="MESPEPTIDES", pepe="PEPEPEP")
pepTab1 <- makeFragments(protTab=protP2, minFra=6, internFr=TRUE, massTy="mono")
cou1 <- countPotModifAAs(pepTab=pepTab1, modTy=list(basMod=c("b","y"),
  varMod=c("p","h")))
modTy2 <- list(basMod=c("b","y","h"), varMod=c("x","p","o","q","e","j"))
cou2 <- countPotModifAAs(pepTab=pepTab1, modTy=modTy2)

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.