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,
      display_msstats = 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`
`printPDF` | (logical) if `TRUE` (default), prints out pdf
`display_msstats` | (logical) if `TRUE`, prints MSstats outputs (default is `FALSE`)
`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

    ## Not run:
    artmsQuantification(yaml_config_file = "path/to/artms-ab-config.yaml")

    ## End(Not run)

[Package artMS version 1.8.3 Index]