summarise_stats: Summarize DEA and/or differential detection results in a...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Summarize DEA and/or differential detection results in a dataset into a table with a single statistic per gene

Description

In most cases, you probably want to use the export_stats_genesummary() function instead. That is a wrapper function that uses this function but also adds additional functionality. For documentation on the output table, also refer to that function.

Usage

summarise_stats(
  dataset,
  return_dea = TRUE,
  return_diffdetect = FALSE,
  dea_logfc_as_effectsize = FALSE,
  diffdetect_zscore_threshold = 6,
  diffdetect_type = "auto"
)

Arguments

dataset	dataset where dea() and/or differential_detect() has been applied
return_dea	boolean, set to TRUE to include DEA results in the stats table that returns 1 value per gene (setting TRUE for both DEA and DD will merge results)
return_diffdetect	analogous to return_dea, but setting this to TRUE includes differential detection results
dea_logfc_as_effectsize	optionally, the resulting effectsize column can be populated with standardized foldchange values (effectsize = log2fc / sd(log2fc)). When including differential detection results this'll be a convenient approach to getting 1 standardized distribution of DEA+DD effectsizes that can be used in e.g. GO analyses. While this is unusual, one could e.g. use this for DEA algorithms that apply shrinkage to estimated foldchanges such as MSqRob
diffdetect_zscore_threshold	differential detect z-score cutoff. A typical value would be 5 or 6 (default) To plot histograms of the respective z-score distributions and inspect potential cutoff values for this relatively arbitrary metric, see below example code
diffdetect_type	type of differential detect scores. options: 'auto' = set to 'detect' if this score is available, 'quant' otherwise 'detect' = differential detection z-scores computed from only "detected" peptides (no MBR) 'quant' = differential detection z-scores computed from all quantified peptides (uses MBR)

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.