SkylinetoMSstatsLiPFormat {MSstatsLiP} | R Documentation

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

### Description

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

### Usage

    SkylinetoMSstatsLiPFormat(
      LiP.data,
      TrP.data = NULL,
      annotation = NULL,
      removeiRT = TRUE,
      filter_with_Qvalue = TRUE,
      qvalue_cutoff = 0.01,
      useUniquePeptide = TRUE,
      removeFewMeasurements = TRUE,
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Feature = FALSE,
      use_log_file = FALSE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL
    )

### Arguments

`LiP.data` | name of LiP Skyline output, which is long-format.
`TrP.data` | name of TrP Skyline output, which is long-format.
`annotation` | name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
`removeiRT` | TRUE (default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them.
`filter_with_Qvalue` | TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
`qvalue_cutoff` | Cutoff for DetectionQValue. 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.
`removeOxidationMpeptides` | TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
`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.
`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 saved to a 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.

### Value

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

### Examples

    ## Output will be in format
    head(MSstatsLiP_data[["LiP"]])
    head(MSstatsLiP_data[["TrP"]])

[Package MSstatsLiP version 1.0.0 Index]