run.diann: Runs a DIA-NN analysis of the selected DIA-file and input...
In MarcIsak/MSLibrarian: What the Package Does (One Line, Title Case)

run.diann

R Documentation

Runs a DIA-NN analysis of the selected DIA-file and input library in TSV format

Description

Runs a DIA-NN analysis of the selected DIA-file and input library in TSV format

Usage

run.diann(
  diannPath,
  diaFile,
  libFile,
  output = NULL,
  matrices = T,
  matQ = 0.01,
  threads = detectCores(),
  fasta = NULL,
  enzyme,
  separateMassAcc = F,
  massAcc = NULL,
  reportLibInfo = T,
  robustLC = NULL,
  relaxProtInf = F,
  carbamidomethyl_C = T,
  nativeLib = F,
  matchBetweenRuns = F
)

Arguments

`diannPath`	Absolute path to the DIA-NN executable
`diaFile`	Absolute path to the input DIA raw file
`libFile`	Absolute path to the input spectral library file (as given by the make.osw.lib function)
`output`	Desired file name for DIA-NN reports (incl. absolute path)
`matrices`	A logical determining if quantitative matrices for proteins and precursors should be outputted (Default=TRUE).
`matQ`	numeric in the range c(0,1) setting the q-value to use for filtering matrices.
`threads`	Integer specifying the number of threads for the analysis
`fasta`	Absolute path to a FASTA file for matching of peptides sequences to proteins
`enzyme`	Character specifying the enzyme to use for in-silico digestion of sequences in the FASTA file
`separateMassAcc`	should mass accuracy be determined for each individual MS file (logical)
`massAcc`	Numeric setting the desired MS1 accuracy
`reportLibInfo`	Logical determining if extra info on fragment ions and precursors should be saved to main report (default TRUE)
`robustLC`	Specfies whether Quantification should be run in Robust LC mode. Possible values are "high_accuracy" or "high_precision". Default = NULL.
`relaxProtInf`	Logical determining if relaxed protein inference should be enabled. Default = FALSE
`carbamidomethyl_C`	Carbamidomethyl on Cysteine residues as fixed modification. Default = T.
`nativeLib`	Logical setting if the spectral library is a native library or not.
`matchBetweenRuns`	logical determining if match-between-runs (MBR) should be enabled. (Default = FALSE)