dot-evalIsoFra: Evaluate Selected Lines Of PepTab

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

Evaluate Selected Lines Of PepTab

Description

Evaluate selected lines of pepTab of SAME AA-length AND iso-mass for preferential cutting sites.

Usage

.evalIsoFra(
  x,
  prefFragPat = NULL,
  seqCol = "seq",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

x	(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)

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")))
.evalIsoFra(peTab)

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