differential_detect: Compare the number of peptide detection counts between groups

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Compare the number of peptide detection counts between groups

Description

The computation of scores is detailed in the online vignitte for "differential testing".

Usage

differential_detect(
  dataset,
  min_peptides_observed = 1L,
  min_samples_observed = 3,
  min_fraction_observed = 0.5,
  count_mode = "auto",
  rescale_counts_per_sample = TRUE,
  return_wide_format = FALSE
)

Arguments

dataset	a valid dataset
min_peptides_observed	minimum number of peptides for a protein to pass filtering rules (i.e. otherwise, no z-score is computed)
min_samples_observed	minimum number of samples where a protein should be observed with at least min_peptides_observed peptides (in either group) when comparing a contrast of group A vs B
min_fraction_observed	for differential detection only; analogous to diffdetect_min_samples_observed, but here you can specify the fraction of samples where a protein needs to be detected in either group (within the respective contrast). default; 0.5 (50% of samples)
count_mode	whether z-scores for only detected peptides, or all observed peptides, should be computed. options; "auto", "detect", "quant"
rescale_counts_per_sample	boolean, indicating whether per sample, detect counts should be rescaled (i.e. to normalize across samples for the number of detected peptides)
return_wide_format	boolean, return table in simplified wide-format (TRUE) or return all data in long-format table (FALSE, default)

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