R: Evaluate selected lines of pepTab (iso-mass) for preferential...

evalIsoFragm {wrTopDownFrag}

R Documentation

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,
  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
`callFrom`	(character) allows easier tracking of message(s) produced

Value

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

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)