artmsEvidenceToSaintExpress {artMS} | R Documentation

## MaxQuant evidence file to SAINTexpress format

### 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.

### Usage

    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)

[Package artMS version 1.6.5 Index]