artmsQuantification {artMS} | R Documentation

## Relative quantification using MSstats

### Description

Relative quantification using MSstats including:

- plots

- quantifications (log2fc, pvalues, etc)

- normalized abundance values

### Usage

    artmsQuantification(
      yaml_config_file,
      data_object = FALSE,
      printPDF = TRUE,
      printTables = TRUE,
      display_msstats = FALSE,
      return_results_object = FALSE,
      verbose = TRUE
    )

### Arguments

`yaml_config_file` | (char, required) The yaml file name and location
`data_object` | (logical) flag to indicate whether the configuration file is a string to a file that should be opened or config object (yaml). Default is `FALSE`. Choose `TRUE` if `yaml_config_file` is a yaml object
`printPDF` | (logical) if `TRUE` (default), prints out pdf
`printTables` | (logical) `TRUE` (default) print results tables
`display_msstats` | (logical) if `TRUE`, prints MSstats outputs (default is `FALSE`)
`return_results_object` | (logical) Default is `FALSE`. If `TRUE`, it returns a list of data frames with MSstats results, including: `comparisonResult`: comparison results `ModelQC` `FittedModel`: fit model details `power`: power calculations `sample_size`: sample size estimations
`verbose` | (logical) `TRUE` (default) shows function messages

### Value

The relative quantification of the conditions and comparisons specified in the keys/contrast file resulting from running MSstats, in addition to quality control plots (if selected)

### Examples

    # Recommended
    # artmsQuantification(yaml_config_file = "your-config-file.yaml")

    # Example to test this function using the example dataset available in artMS
    # Step 1: Add evidence, keys, and contrast to configuration object
    artms_data_ph_config$files$evidence <- artms_data_ph_evidence
    artms_data_ph_config$files$keys <- artms_data_ph_keys
    artms_data_ph_config$files$contrasts <- artms_data_ph_contrast

    # Step 2: Run the quantification step
    quant_results <- artmsQuantification(yaml_config_file = artms_data_ph_config,
                                         data_object = TRUE,
                                         display_msstats = FALSE,
                                         printPDF = FALSE,
                                         printTables = FALSE)
    # Check the list of data frames "quant_results". Nothing should be printed out.

[Package artMS version 1.10.2 Index]