Relative quantification using MSstats including:

  • plots

  • quantifications (log2fc, pvalues, etc)

  • normalized abundance values

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

Arguments

yaml_config_file

(char) 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)

printPDF

(logical) if TRUE, prints out pdf

display_msstats

(logical) if TRUE, prints MSstats outputs

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

# \donttest{ artmsQuantification(yaml_config_file = "path/to/artms-ab-config.yaml")
#> Warning: cannot open file 'path/to/artms-ab-config.yaml': No such file or directory
#> Error in readLines(con): cannot open the connection
# }