artmsQuantification: Relative quantification using MSstats

In artMS: Analytical R tools for Mass Spectrometry

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)

artMS documentation built on April 14, 2021, 6 p.m.