dot-countModif: Count For All Proteins The Occurance Of Modification Types

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

Count For All Proteins The Occurance Of Modification Types

Description

Count for all protein 'sequ' the occurance of modification types defined in list 'modTyp' (only if in names(specAAMod)).

Usage

.countModif(
  sequ,
  modTyp,
  specAAMod,
  knownMods,
  detailedCount = FALSE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

sequ	(character) peptide sequence(s)
modTyp	(list) modifications : $basMod for character vector of fixed modifications and $varMod for variable modifications. For one letter-code see AAfragSettings("modChem")
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)
detailedCount	(logical)
silent	(logical) suppress messages
debug	(logical) for bug-tracking: more/enhanced messages and intermediate objects written in global name-space
callFrom	(character) allow easier tracking of message(s) produced

Value

This function returns a 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")
modTy2 <- list(basMod=c("b","y","h"), varMod=c("x","p","o","q","e","j"))
.countModif(pepTab1[,2], modTyp=c("b","y"), specAAMod=AAfragSettings(outTy="all")$specAAMod, 
  knownMods=AAfragSettings(outTy="all")$knownMods)

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