evalIsoFragm: Evaluate Selected Lines Of PepTab (iso-mass) For Preferential...

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

Evaluate Selected Lines Of PepTab (iso-mass) For Preferential Cutting Sites

Description

Evaluate selected lines of pepTab (iso-mass) for preferential cutting sites. Such sites are taken by default from .prefFragPattern() simplified from a publication by the Kelleher group (Haverland 2017, J Am Soc Mass Spectrom) or can be furnished by the user.

Usage

evalIsoFragm(
  z,
  prefFragPat = NULL,
  seqCol = "seq",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

z	(matrix) main input, must contain cols specified as seqCol and "no","tailAA","precAA"
prefFragPat	(matrix) specifies preferential fragmentation (which combination of AA to consider cols cTer,nTer,score), default made by .prefFragPattern()
seqCol	(character) column names for the column containing the sequence to search for preferential cutting sites
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function returns line ID-numbers (pepTab[,"no"]) for those below median score (ie to remove from pepTab) or NULL if nothing to remove due to preferential fragmentation

See Also

makeFragments

Examples

peTab <- matrix(c("9","13","14","15", "LPVIAGHEAAG","PVIAGHEAAGI","EKKPFSI","KKPFSIE", 
  "P","L","E","E", "I","V","E","E"),nr=4,dimnames=list(NULL,c("no","seq","precAA","tailAA")))
evalIsoFragm(peTab)

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