artmsQuantification: Relative quantification using MSstats

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

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. 

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.