SkylinetoMSstatsLiPFormat: Converts raw LiP MS data from Skyline into the format needed...

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

Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP.

Description

Takes as as input both raw LiP and Trp outputs from Skyline.

Usage

SkylinetoMSstatsLiPFormat(
  LiP.data,
  TrP.data = NULL,
  annotation = NULL,
  msstats_format = FALSE,
  removeiRT = TRUE,
  filter_with_Qvalue = TRUE,
  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.
msstats_format	logical indicating how the data was output from Skyline. FALSE (default) indicates that standard Skyline output was selected. TRUE should be selected if the Skyline data was output using the MSstats format option in Skyline.
removeiRT	TRUE (default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for DetectionQValue. default is 0.01.
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.