wrTopDownFrag (version 1.0.4)

randMassByMut: Make decoy mass by full randomization

Description

Make full random decoy mass vector (mimick pepTab)

Usage

randMassByMut(
  pepTab,
  randCha,
  useCol = "mass",
  negAvoid = TRUE,
  sepCol = FALSE,
  inDel = FALSE,
  nAlter = 1,
  setSeed = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a matrix with additional column 'decoyMass', or if 'sepCol'=FALSE as additional lines

Arguments

pepTab

(matrix) typically table of petides, one column should match 'useCol' for numeric mass values

randCha

(numeric) vector of possible mass alterations for random drawing

useCol

(character) column from 'pepTab' with mass values to make decoys

negAvoid

(logical) if TRUE try avoiding 0 or negative random mass in result

sepCol

(character) optional column from 'pepTab'

inDel

(logical) switch to make random mass by insertion/deletion of 1 AA

nAlter

(integer) number of alterations per peptide

setSeed

(character) seed for random number generation set.seed()

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

randMassByStochastic

Examples

pepTab1 <- cbind(no=11:12, seq=c("YVVDTS","YVVDTSK"), origNa="test.P000",
  ty=c("inter","Cter"),mass=c(681.308997360991,809.403960378691))
randMassByMut(pepTab1, corMutShift())
randMassByMut(pepTab1, corInDelShift(), inDel=TRUE)