ms_process: Process mass spectrometry data

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Process mass spectrometry data

Description

Process mass spectrometry data for filtering out contaminant samples, manipulating variables, removing duplicates, and more.

Usage

ms_process(
  psm,
  protein,
  treatment,
  samples = NULL,
  sample.id = NULL,
  path = NULL,
  ...
)

Arguments

psm	PSM file
protein	Protein file
treatment	character vector of treatment groups
samples	character vector of sample names to keep
sample.id	character vector for sample IDs. Order of samples must match that in the psm raw data.
path	file path to save return element pep
...	additional arguments to ms_condition

Value

A list with the following elements

pep	processed data frame to be used by ms_summarize
raw	raw data values
l2	log2 raw data values
vsn	vsn raw data values

Author(s)

Derek Chiu

See Also

Other Mass Spectrometry functions: ms_condition(), ms_plot, ms_summarize(), ms_top()

TalhoukLab/biostatUtil documentation built on April 14, 2025, 4:15 a.m.