wrProteo: razorNoFilter – R documentation

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razorNoFilter

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,
  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
`callFrom`	(character) allows easier tracking of messages produced

Value

vector of logical values if corresponding line passes filter criteria

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

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release