wrTopDownFrag (version 1.0.4)

scorePrefFrag: Identifcation and scoring of preferential cuting sites

Description

Search for preferential fragmentation sites from 'pepTab' among the 3 colums specified via 'useCol' (for full AA sequence, preceeding AA, tailing AA) and return sum of scores (from 3rd column of prefFragPat) for both ends. Note : proteins must be witten as single lettre code.

Usage

scorePrefFrag(
  pepTab,
  useCol = c("seq", "precAA", "tailAA"),
  prefFragPat = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a matrix with fragment sequence, mass, start- and end-position, heading and tailing AA (or NA if terminal fragment)

Arguments

pepTab

(matrix) peptide-fragments with lines for peptides, cols as sequence/preceedingAA/tailingAA

useCol

(character) column names for peptide-sequence,preceeding and tailing AA

prefFragPat

(matrix) for preferential fragmentation rules (see .prefFragPattern())

silent

(logical) suppress messages

debug

(logical) additional messages and objects exportet to current session for debugging

callFrom

(character) allow easier tracking of messages produced

See Also

makeFragments

Examples

pepT <- cbind(precAA=c("A","D","D","A","D"),seq=c("AKA","PKA","AKA","PKD","PKD"),
  tailAA=c("A","A","D","P","P"))
scorePrefFrag(pepT)