artmsEvidenceToSAINTq {artMS} | R Documentation

## MaxQuant evidence file to SAINTq format

### 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)

### Usage

    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

### 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`

### Value

The input files requires to run SAINTq

### Examples

    # Testing that the files cannot be empty
    artmsEvidenceToSAINTq   (evidence_file = NULL,
                                       keys_file = NULL,
                                       output_dir = NULL)

[Package artMS version 1.6.5 Index]