# 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"