Process mass spectrometry data — ms_process • biostatUtil

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

See also

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

Author

Derek Chiu