SpectronauttoMSstatsFormat {MSstats} | R 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)

[Package MSstats version 4.1.1 Index]