compareDiannResultSets: compareDiannResultSets

In heuselm/mocode: Integrates MS-based-proteomics Data Analysis Code

compareDiannResultSets

Description

Comparison of DIANN resultsets stored side-by-side in a result folder, e.g. Results from pass1 analysis and pass2 re-analysis (Match Between Runs) or results obtained using different input spectral libraries. Compares the ID numbers from stats.tsv, but also the ID numbers obtained on protein group level by counting from the quantitative tables. Compares sets on identified proteins in Venn Diagrams and their quantitative patterns in side-by-side heatmap. Further, pairwise sample-sample correlation for a subset of runs is implemented, however currently not experimental-design-aware.

Usage

compareDiannResultSets(
  result_folder = "./",
  Venn_diagram = TRUE,
  compare_precursor_level = FALSE,
  heatmap = TRUE,
  sample_correlation = TRUE
)

Arguments

result_folder	Path to the result folder. All resultsets identified by their *.stats.tsv file will be analyzed.
Venn_diagram	Whether to calculate and draw Venn diagrams from the sets of analytes detected
compare_precursor_level	Whether to include precursor level comparisons in Venn and heatmap. This might be slow for calculation of heatmap, defaults to FALSE.
heatmap	Whether to calculate and draw heatmaps, defaults to true. These are the most informative plots..
sample_correlation	Whether to calculate sample-sample correlation and output heatmap and xy scatters on subset

Value

Returns a combined data.table of merged quantitative results with extra column resultset

heuselm/mocode documentation built on Oct. 23, 2023, 8:43 a.m.