ms_summarize: Summarize mass spectrometry data

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Summarize mass spectrometry data

Description

Summarize mass spectrometry data for expression differences between sample groups. Apply Benjamini-Hochberg p-value adjustment.

Usage

ms_summarize(
  x,
  g,
  level = c("Gene", "Peptide"),
  col.names = NULL,
  info.vars = NULL,
  path = NULL
)

Arguments

x	data frame with expression values
g	vector of factor levels for samples
level	analysis is on the "Gene" level or "Peptide" level
col.names	vector of column names for output data frame
info.vars	vector of column names containing metadata information. These variables are collapsed if not unique.
path	file path to save result object

Details

Gene-level analysis is performed on the "Gene" variable. Peptide-level analysis is performed on distinct combinations of the Accession, Gene, Descriptions, Sequence, and Modifications variables. This combined variable is renamed to "AGDSM".

Value

A data frame of statistics from analyzing mass spec data. Includes t-values, Wald p-values, effect sizes, fold change, absolute fold change.

Author(s)

Derek Chiu

See Also

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

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