DIANNtoMSstatsFormat: Import Diann files

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Import Diann files

Description

Import Diann files

Usage

DIANNtoMSstatsFormat(
  input,
  annotation = NULL,
  global_qvalue_cutoff = 0.01,
  qvalue_cutoff = 0.01,
  pg_qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = TRUE,
  removeProtein_with1Feature = TRUE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  MBR = TRUE,
  quantificationColumn = "FragmentQuantCorrected",
  ...
)

Arguments

input	name of MSstats input report from Diann, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run.
global_qvalue_cutoff	The global qvalue cutoff
qvalue_cutoff	local qvalue cutoff for library
pg_qvalue_cutoff	local qvalue cutoff for protein groups Run should be the same as filename.
useUniquePeptide	should unique pepties be removed
removeFewMeasurements	should proteins with few measurements be removed
removeOxidationMpeptides	should peptides with oxidation be removed
removeProtein_with1Feature	should proteins with a single feature be removed
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.
MBR	True if analysis was done with match between runs
quantificationColumn	Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Elijah Willie

Examples

input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
                                package="MSstatsConvert")
annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
                                package = "MSstatsConvert")
input = data.table::fread(input_file_path)
annot = data.table::fread(annotation_file_path)
output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, 
                                use_log_file = FALSE)
head(output)

Vitek-Lab/MSstatsConvert documentation built on Nov. 21, 2024, 12:23 p.m.