DIAUmpiretoMSstatsFormat: Import DIA-Umpire files

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Import DIA-Umpire files

Description

Import DIA-Umpire files

Usage

DIAUmpiretoMSstatsFormat(
  raw.frag,
  raw.pep,
  raw.pro,
  annotation,
  useSelectedFrag = TRUE,
  useSelectedPep = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

raw.frag	name of FragSummary_date.xls data, which includes feature-level data.
raw.pep	name of PeptideSummary_date.xls data, which includes selected fragments information.
raw.pro	name of ProteinSummary_date.xls data, which includes selected peptides information.
annotation	name of annotation data which includes Condition, BioReplicate, Run information.
useSelectedFrag	TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.
useSelectedPep	TRUE will use the selected peptide for each protein. 'Selected_peptides' column is required.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
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.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
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 added to an existing log 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.
...	additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

diau_frag = system.file("tinytest/raw_data/DIAUmpire/dia_frag.csv", 
                             package = "MSstatsConvert")
diau_pept = system.file("tinytest/raw_data/DIAUmpire/dia_pept.csv", 
                             package = "MSstatsConvert")
diau_prot = system.file("tinytest/raw_data/DIAUmpire/dia_prot.csv", 
                             package = "MSstatsConvert")
annot = system.file("tinytest/annotations/annot_diau.csv", 
                    package = "MSstats")
diau_frag = data.table::fread(diau_frag) 
diau_pept = data.table::fread(diau_pept) 
diau_prot = data.table::fread(diau_prot) 
annot = data.table::fread(annot)
diau_frag = diau_frag[, lapply(.SD, function(x) if (is.integer(x)) as.numeric(x) else x)]
# In case numeric columns are not interpreted correctly

diau_imported = DIAUmpiretoMSstatsFormat(diau_frag, diau_pept, diau_prot, 
                                         annot, use_log_file = FALSE)
head(diau_imported)

MeenaChoi/MSstats documentation built on Nov. 30, 2024, 7:26 a.m.