Summarize mass spectrometry data

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

Value

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

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".

See also

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

Author

Derek Chiu