filter.proteins: Subsets a spectral library based on a selection of protein...
In MarcIsak/MSLibrarian: What the Package Does (One Line, Title Case)

filter.proteins

R Documentation

Subsets a spectral library based on a selection of protein IDs

Description

Subsets a spectral library based on a selection of protein IDs

Usage

## S3 method for class 'proteins'
filter(
  inputLib = NULL,
  outputLib = NULL,
  type = NULL,
  calibrationLib = NULL,
  fdr,
  diaFiles,
  diannPath = NULL,
  replace = F
)

Arguments

`inputLib`	path to an input spectral library
`outputLib`	desired path to a subset output spectral library
`type`	means of selecting protein IDs. Possible values are 1) "calibrationlibrary" 2) "diann" or 3) custom character vector of protein IDs.
`calibrationLib`	path to a calibration library object (*.RData). This argument is only used if type == "calibrationlibrary"
`fdr`	numeric decimal value giving the protein group fdr cutoff to use for filtering (default = 0.2, 0 < fdr <= 1).
`diaFiles`	character vector to DIA MS files in .raw format.
`diannPath`	path to DIA-NN executable. Only used if type == "diann". If no path is given, the function will try to auto-detect the DIA-NN installation.
`replace`	should the input library be overwritten/replaced (logical)? Default is FALSE