create.calibration.lib: Creates a calibration library from a set of DIA files and a...
In MarcIsak/MSLibrarian: What the Package Does (One Line, Title Case)

create.calibration.lib

R Documentation

Creates a calibration library from a set of DIA files and a FASTA file

Description

Creates a calibration library from a set of DIA files and a FASTA file

Usage

create.calibration.lib(
  diaFiles = NULL,
  fasta,
  projectFolder,
  msConvert = NULL,
  tppDir = NULL,
  openMsDir = NULL,
  msfragger = NULL,
  searchEngine = "comet",
  filter = "peakPicking true 1-",
  staggeredWindows = F,
  diaUmpireParams = NULL,
  cometParams = NULL,
  spectrastParams = NULL,
  fragParams = NULL,
  libType = "consensus",
  updateSearch = FALSE,
  updateLib = FALSE,
  irt = NULL,
  threads = detectCores()
)

Arguments

`diaFiles`	*Input DIA MS files in either RAW or mzXML format
`fasta`	*FASTA file to use for database searching in Comet.
`projectFolder`	*Name of project folder (absolute path). It must be unique.
`msConvert`	path to msConvert executable. If no argument is passed, it will try to autodetect the executable on your system.
`tppDir`	path to Transproteomic pipeline installation folder (for example "C:/TPP"). if no argument is passed, it will try to autodetect the installation folder.
`openMsDir`	path to OpenMS installation folder.(such as "C:/Program Files/OpenMS-2.5.0/"). Will try to autodetect the installation folder if no argument is passed.
`msfragger`	path to MSFragger java application.
`searchEngine`	character specifying the search engine to use. Can be either "comet" (default) or "msfragger".
`filter`	character vector with msCOnvert filters. Peakpickning on the MS1 level is set as default.
`staggeredWindows`	logical stating if staggered windows were acquired for the input DIA files. (Default is FALSE).
`diaUmpireParams`	*path to a DIA Umpire Signal extraction parameters file. These parameters are necessary for the creation of Pseudo-DDA MS/MS spectra.
`cometParams`	*path to a Comet parameters file necessary for the database searching of pseudo-MS/MS spectra.
`spectrastParams`	*path to a spectrast parameters file with parameters for creation of a spectral library.
`fragParams`	*path to a Comet parameters file necessary for the database searching of pseudo-MS/MS spectra.
`libType`	Type of library to build. Possible values are 1) 'consensus' (default) and 2) 'best_replicate'
`updateSearch`	logical indicating if the database searching should be updated.
`updateLib`	logical indicating if the created library should be updated. Will in this case re-run Spectrast and OpenSwathAssayGenerator to make a new library.
`irt`	Can either be set to "biognosys_irt", "CiRT" or NULL (default). If set to "biognosys_irt" or "CiRT", the calibration library retention times will be converted to iRT values.
`threads`	Number of threads or parallel processes to use. Will by default use all available logical processors.