DIANNtoMSstatsLiPFormat: Converts raw LiP MS data from DIA-NN into the format needed...

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP.

Description

Takes as as input both raw LiP and Trp outputs from DIA-NN

Usage

DIANNtoMSstatsLiPFormat(
  lip_data,
  trp_data = NULL,
  annotation = NULL,
  global_qvalue_cutoff = 0.01,
  qvalue_cutoff = 0.01,
  pg_qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Feature = FALSE,
  use_log_file = FALSE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

lip_data	name of LiP Skyline output, which is long-format.
trp_data	name of TrP Skyline output, which is long-format.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
global_qvalue_cutoff	The global qvalue cutoff. Default is 0.01.
qvalue_cutoff	Cutoff for DetectionQValue. Default is 0.01.
pg_qvalue_cutoff	local qvalue cutoff for protein groups Run should be the same as filename. Default is .01.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be saved to a file.
verbose	logical. If TRUE, information about data processing wil be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.

Value

a list of two data.frames in MSstatsLiP format

Examples

## Output will be in format
head(MSstatsLiP_data[["LiP"]])
head(MSstatsLiP_data[["TrP"]])

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.