Relative quantification using MSstats

Source: R/main.R

Relative quantification using MSstats including:

  • plots

  • quantifications (log2fc, pvalues, etc)

  • normalized abundance values

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)

#> --------------------------------------------
#> artMS: Relative Quantification using MSstats
#> --------------------------------------------
#> >> Reading the configuration file
#> >> LOADING DATA 
#> >> MERGING FILES 
#> >> CONVERT Intensity values < 1 to NA
#> >> FILTERING 
#> -- Contaminants CON__|REV__ removed
#> -- Removing protein groups
#> -- Use <Leading.razor.protein> as Protein ID
#> >> CONVERTING THE DATA TO MSSTATS FORMAT 
#> -- Selecting Sequence Type: MaxQuant 'Modified.sequence' column
#> 	(+) <Fraction> column added (with value 1, MSstats requirement)
#> -- Adding NA values for missing values (required by MSstats) 
#> >> RUNNING MSstats (it usually takes a 'long' time: please, be patient)
#> 	(MSstats messages are turned off. Select <display_msstats = TRUE> to activate MSstats outputs)
#> >> MSstats done
# Check the list of data frames "quant_results". Nothing should be printed out.