razorNoFilter: Filter based on either number of total peptides and specific...

In wrProteo: Proteomics Data Analysis Functions

Filter based on either number of total peptides and specific peptides or number of razor petides

Description

razorNoFilter filters based on either a) number of total peptides and specific peptides or b) numer of razor petides. This function was designed for filtering using a mimimum number of (PSM-) count values following the common practice to consider results with 2 or more peptide counts as reliable. The function be (re-)run independently on each of various questions (comparisons). Note: Non-integer data will be truncated to integer (equivalent to floor).

Usage

razorNoFilter(
  annot,
  speNa = NULL,
  totNa = NULL,
  minRazNa = NULL,
  minSpeNo = 1,
  minTotNo = 2,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

annot	(matrix or data.frame) main data (may contain NAs) with (PSM-) count values for each protein
speNa	(integer or character) indicate which column of 'annot' has number of specific peptides
totNa	(integer or character) indicate which column of 'annot' has number of total peptides
minRazNa	(integer or character) name of column with number of razor peptides, alternative to 'minSpeNo'& 'minTotNo'
minSpeNo	(integer) minimum number of pecific peptides
minTotNo	(integer) minimum total ie max razor number of peptides
silent	(logical) suppress messages
debug	(logical) display additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function returns a vector of logical values if corresponding line passes filter criteria

See Also

presenceFilt

Examples

set.seed(2019); datT <- matrix(sample.int(20,60,replace=TRUE), ncol=6,
  dimnames=list(letters[1:10], LETTERS[1:6])) -3
datT[,2] <- datT[,2] +2
datT[which(datT <0)] <- 0
razorNoFilter(datT, speNa="A", totNa="B")

wrProteo documentation built on April 12, 2025, 1:16 a.m.