MaxQuant evidence file to SAINTexpress format — artmsEvidenceToSaintExpress • artMS
Description: Converts the MaxQuant evidence file to the 3 required files by SAINTexpress. One can choose to either use the spectral counts (use msspc) or the intensities (use msint) for the analysis.

# MaxQuant evidence file to SAINTexpress format

Source: `R/evidenceToSaintExpressFormat.R`
`artmsEvidenceToSaintExpress.Rd`

Converts the MaxQuant evidence file to the 3 required files by SAINTexpress. One can choose to either use the `spectral counts` (use `msspc`) or the `intensities` (use `msint`) for the analysis.

    artmsEvidenceToSaintExpress(
      evidence_file,
      keys_file,
      ref_proteome_file,
      quant_variable = c("msspc", "msint"),
      output_file,
      verbose = TRUE
    )

## Arguments

evidence_file | (char) The evidence file path and name
keys_file | (char) Keys file with a SAINT column specifying test (`T`) and control (`C`) conditions
ref_proteome_file | (char) Reference proteome path file name in fasta format
quant_variable | (char) choose either `msspc` (spectral counts, default) or `msint` (MS Intensity)
output_file | (char) Output file name (must have extension .txt)
verbose | (logical) `TRUE` (default) shows function messages

## Value

The 3 required files by SAINTexpress:

- `interactions.txt`

- `preys.txt`

- `baits.txt`

## Examples

    # Testing that the files cannot be empty
    artmsEvidenceToSaintExpress(evidence_file = NULL,
    keys_file = NULL, ref_proteome_file = NULL)
    #> >> CONVERTING TO SAINTexpress FORMAT #> [1] "The evidence_file, keys_file, and ref_proteome_file \n           must not be empty"