randMassByMut: Make decoy mass by full randomization

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

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
)

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

Value

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

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)

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