mod.spectral.lib: Modifies and filters a spectral library on protein, peptide,...

In MarcIsak/MSLibrarian: What the Package Does (One Line, Title Case)

Modifies and filters a spectral library on protein, peptide, or transition level. Also allows for changing library retention times.

Description

Modifies and filters a spectral library on protein, peptide, or transition level. Also allows for changing library retention times.

Usage

mod.spectral.lib(
  projectFolder = NULL,
  inputLib = NULL,
  outputLib = NULL,
  calibrationLib = NULL,
  mods,
  diaFiles,
  protMod,
  protFdr = 0.05,
  diannPath = NULL,
  topPept = NULL,
  pregoPath = NULL,
  cutoffTrans = NULL,
  topTrans = NULL,
  minTrans = NULL,
  nCal = 0.25,
  deepLcPath = NULL
)

Arguments

projectFolder	path to a MSLibrarian project folder
inputLib	path to an input spectral library. If there is only one library, it will be selected automatically if arg - projectFolder is supplied.
outputLib	desired path to a modified spectral library. A default name is generated if not specified.
calibrationLib	path to a Calibration Library (*.RData format)
mods	character vector specifying the modifications to apply. c("protein", "peptide", "transitions", "rt")
diaFiles	path to DIA MS raw files used to build the calibration library
protMod	type of protein modification to apply. Possible values are 1) "calibrationlibrary", 2) "diann" or 3) a character vector of Uniprot identfiers
protFdr	decimal number between 0 - 1 giving the protein group FDR to use for protein ID subsetting of a library.
diannPath	path to DIA-NN executable. If not supplied, the function will try to auto-detect the executable on your system.
topPept	integer giving the maximum number of high responding peptides (as given by PREGO), to allow for each protein group.
pregoPath	path to PREGO executable. If not supplied, the function will try to auto-detect the executable on your system.
cutoffTrans	decimal number between 0 - 1 giving the minimum relative intensity that a transition can have (0.05 is default).
topTrans	maximum number of high intensity transitions to allow for each precursor in the library. (Is ignored/NULL by default)
minTrans	minimum number of transitions to allow for each precursor in a library.
nCal	decimal number giving the proportion of calibration library entries to use for RT calibration in DeepLC. (0.25 by default)
deepLcPath	path to DeepLC GUI folder. It will try to auto-detect the folder if not supplied.

MarcIsak/MSLibrarian documentation built on Aug. 27, 2022, 4:55 a.m.