dot-checkModTy: Check Modification Type

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

Check Modification Type

Description

Check Modification Type

Usage

.checkModTy(
  modTy,
  knownMods,
  phoDePho = c("p", "q"),
  modTyGr = c("basMod", "varMod"),
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

modTy	(character) list of modification types to be considered
knownMods	(character) optonal custom list of known modifications, default from AAfragSettings(outTy="all")$knownMods
phoDePho	(character) names of modifications that may be de-phosphorylated
modTyGr	(character) groups of modifications to consider (defaults used both 'basMod' and 'varMod')
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allows easier tracking of messages produced

Value

This function returns the corrected list of mixed of variable and fixed modifications ($basMod, $varMod and $varMo2)

See Also

AAfragSettings

Examples

modTy1 <- list(basMod=c("b","y","h"),varMod=c("p","o","q"))
.checkModTy(modTy1, knownMods=c("a","b","h","o","p","q","y"))

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