Filtering proteins or contaminants

Apply a series of filtering steps to the data set.

Usage

filterOutIn(
  dataSet,
  listName = c(),
  regexName = c(),
  by = NULL,
  removeList = TRUE,
  saveRm = TRUE
)

Arguments

dataSet

The 2d data set of experimental values.

listName

A character vector of text strings used as keys for selecting or removing.

regexName

A character vector specifying proteins for regular expression pattern matching to select or remove.

by

A character string (default = "PG.ProteinName" for Spectronaut, default = "AccessionNumber" for Scaffold) specifying the information to which listName and/or regexName filter is applied. Allowable options include:

• For Spectronaut: "PG.Genes", "PG.ProteinAccession", "PG.ProteinDescriptions", and "PG.ProteinName".

• For Scaffold: "ProteinDescriptions", "AccessionNumber", and "AlternateID".

removeList

A boolean (default = TRUE) specifying whether the list of proteins should be removed or selected.

• TRUE: Remove the list of proteins from the data set.

• FALSE: Remove all proteins not in the list from the data set.

saveRm

A boolean (default = TRUE) specifying whether to save removed data to current working directory. This option only works when removeList = TRUE.

Value

A filtered 2d dataframe.

Details

If both listName and regexName are provided, the proteins selected or removed will be the union of those specified in listName and those matching the regex pattern in regexName.