plot_foldchange_distribution_among_replicates: Plot within-group foldchange distributions to assess outlier...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Plot within-group foldchange distributions to assess outlier samples

Description

Plot within-group foldchange distributions to assess outlier samples

Usage

plot_foldchange_distribution_among_replicates(peptides, samples)

Arguments

peptides	peptide tibble, e.g. dataset$peptides, which must hold raw intensity data in "intensity" column and filtered and normalized data in the column "intensity_qc_basic"
samples	sample tibble, e.g. dataset$samples

Examples

## Not run: 
  dataset = filter_peptides_by_group(
    dataset,
    colname="intensity_qc_basic",
    disregard_exclude_samples = FALSE,
    nquant=2,
    ndetect=1+is_dia_dataset(dataset),
    norm_algorithm = c("vsn", "modebetween_protein"),
    rollup_algorithm = "maxlfq"
  )
  l = plot_foldchange_distribution_among_replicates(mypeptides, dataset$samples)
  for(p in l$plotlist) print(p)
  print(l$tib_scores)

## End(Not run)

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