SpectronauttoMSstatsLiPFormat {MSstatsLiP} | R Documentation

## Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP.

### Description

Takes as as input both raw LiP and Trp outputs from Spectronautt.

### Usage

    SpectronauttoMSstatsLiPFormat(
      LiP.data,
      fasta,
      Trp.data = NULL,
      annotation = NULL,
      intensity = "PeakArea",
      filter_with_Qvalue = TRUE,
      qvalue_cutoff = 0.01,
      useUniquePeptide = TRUE,
      removeFewMeasurements = TRUE,
      removeProtein_with1Feature = FALSE,
      removeNonUniqueProteins = TRUE,
      removeModifications = TRUE,
      removeiRT = TRUE,
      summaryforMultipleRows = max,
      which.Conditions = "all",
      use_log_file = FALSE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      base = "MSstatsLiP_log_"
    )

### Arguments

`LiP.data` | name of LiP Spectronaut output, which is long-format.
`fasta` | A string of path to a FASTA file, used to match LiP peptides.
`Trp.data` | name of TrP Spectronaut output, which is long-format.
`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.
`removeNonUniqueProteins` | TRUE will remove proteins that were not uniquely identified. IE if the protein column contains multiple proteins seperated by ";". TRUE is default
`removeModifications` | TRUE will remove peptide that contain a modification. Modification must be indicated by "[". TRUE is default
`removeiRT` | TRUE will remove proteins that contain iRT. True 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.
`which.Conditions` | list of conditions to format into MSstatsLiP format. If "all" all conditions will be used. Default is "all".
`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 will 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.
`base` | start of the file name.

### Value

a `list` of two `data.frames` in MSstatsLiP format

### Examples

    # Output datasets of Spectronaut
    head(LiPRawData)
    head(TrPRawData)

    fasta_path <- system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP")

    MSstatsLiP_data <- SpectronauttoMSstatsLiPFormat(LiPRawData,
                                                     fasta_path,
                                                     TrPRawData)
    head(MSstatsLiP_data[["LiP"]])
    head(MSstatsLiP_data[["TrP"]])

[Package MSstatsLiP version 1.0.0 Index]