MaxQuant evidence file to SAINTq format — artmsEvidenceToSAINTq • artMS
Description: Converts the MaxQuant evidence file to the required files by SAINTq. The user can choose to use either peptides with spectral counts (use msspc) or the all the peptides (use all) for the analysis. The quantitative can be also chosen (either MS Intensity or Spectral Counts)

# MaxQuant evidence file to SAINTq format

Source: `R/evidenceToSAINTqFormat.R`
`artmsEvidenceToSAINTq.Rd`

Converts the MaxQuant evidence file to the required files by SAINTq. The user can choose to use either peptides with `spectral counts` (use `msspc`) or the all the peptides (use `all`) for the analysis. The quantitative can be also chosen (either MS Intensity or Spectral Counts)

    artmsEvidenceToSAINTq(
      evidence_file,
      keys_file,
      output_dir = "artms_saintq",
      sc_option = c("all", "msspc"),
      fractions = FALSE,
      quant_variable = c("msint", "msspc"),
      verbose = TRUE
    )

## Arguments

evidence_file | (char or data.frame) The evidence file path and name, or data.frame
keys_file | (char) Keys file with a SAINT column specifying test (`T`) and control (`C`) conditions
output_dir | (char) New directory to create and save files. Default is current directory (recommended to provide a new folder name).
sc_option | (char). Filter peptides with spectral counts only. Two options: `msspc`: use only peptides with spectral_counts `all` (default): all peptides detected (including the one resulting from the MaxQuant 'Match between run' algorithm)
fractions | (logical) `TRUE` for 2D proteomics (fractions). Default: `FALSE`
quant_variable | (char) Select the quantitative variable. Two options available: `msint`: MS Intensity (default) `msspc`: MS.MS.count (Spectral Counts)
verbose | (logical) `TRUE` (default) shows function messages

## Value

The input files requires to run SAINTq

## Details

After running the script, the new specified folder should contain the folling files:

- saintq-config-peptides

- saintq-config-proteins

- saintq_input_peptides.txt

- saintq_input_proteins.txt

Then `cd` into the new folder and run either of the following two options (assuming that `saintq` is installed in your linux/unix/mac os x system):

`> saintq config-saintq-peptides`

or

`> saintq config-saintq-proteins`

## Examples

    # Testing that the files cannot be empty
    artmsEvidenceToSAINTq   (evidence_file = NULL,
                                       keys_file = NULL,
                                       output_dir = NULL)
    #> >> GENERATING A SAINTq INPUT FILE #> >> CHECKING THE keys FILE FIRST #> [1] "The evidence_file, keys_file and output_dir must not be NULL"