ms_top: Top variables in mass spectrometry analysis

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Top variables in mass spectrometry analysis

Description

Show top genes/peptides defined by significance level and absolute fold change.

Usage

ms_top(x, level = c("Gene", "Peptide"), alpha = 0.05, fc = 1.25, path = NULL)

Arguments

x	data frame object returned by ms_summarize
level	analysis is on the "Gene" level or "Peptide" level
alpha	significance level
fc	minimum absolute fold change
path	file path to save result object

Details

The input x is the result matrix returned by ms_summarize. We want to filter x such that only interesting variables remain: i.e. those that show statistical significance in an overall test and a scientifically relevant effect size. Variables of interest are summarized either on the gene level or peptide level.

By default, the level of statistical significance is set to 5\ Benjamini-Hochberg adjusted omnibus test p-value. The minimum absolute fold change for determining scientific relevance is 1.25 by default. These default values can be modified for different studies or projects, but offer a general measure of validity for users to start with.

Value

A data frame showing the top variables. If level = "Gene", the return value is a 4 column data frame, showing the Gene, Accession, BH adjusted omnibus p-value, and absolute fold change columns from x. If level = "Peptide", the return value is the same except the Gene and Accession columns are replaced with the AGDSM column from x.

Note

The fold change criterion only needs to be satisfied for one comparison if the experiment has 3 or more sample groups. For example, suppose we have 1 control group and treatments A and B. We filter variables on the fold change criterion where the absolute fold change is greater than fc for either A vs. control or B vs. control.

Author(s)

Derek Chiu

See Also

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

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