SpectronauttoMSstatsFormat: Import Spectronaut files

View source: R/converters.R

SpectronauttoMSstatsFormatR Documentation

Import Spectronaut files

Description

Import Spectronaut files

Usage

SpectronauttoMSstatsFormat(
  input,
  annotation = NULL,
  intensity = "PeakArea",
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input

name of Spectronaut output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed.

annotation

name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Spectronaut, use annotation=NULL (default). It will use the annotation information from input.

intensity

'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut.

filter_with_Qvalue

TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in EG.Qvalue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.

qvalue_cutoff

Cutoff for EG.Qvalue. 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.

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

spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
                              package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_imported = SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE)
head(spectronaut_imported)


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