DIANNtoMSstatsFormat: Import Diann files

View source: R/converters.R

DIANNtoMSstatsFormatR Documentation

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,
  ...
)

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

...

additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Author(s)

Elijah Willie

Examples

## Not run: 
input = fread('diann_pooled_report.tsv')
annot = fread('Annotation.csv')
colnames(annot) = c('Condition', 'Run', 'BioReplicate')
input = DIANNtoMSstatsFormat(input, annotation = annot, MBR = F)
head(input)

## End(Not run)

MeenaChoi/MSstats documentation built on July 13, 2024, 10:59 a.m.