Skip to content

Feature: Add Weighted LCAs

Juliane Schmachtenberg requested to merge weighted_LCAs into master

LCA determination with two different methods:

  1. per protein group (with threshold, default: 1). If the ratio of proteins assigned to an ancestor is at least as high as the threshold, this ancestor is assigned to the entire group (multiple above threshold --> lca with highest support. Changes previous default behaviour. For example if a species/lineage is found for all protein accessions in one group, this species/lineage has a support of 100% and is chosen by the new lca-methode as LCA. Before: if any other species was determined --> various.

  2. democratic (takes the one with highest occurrence in whole task)

New in summary.txt: one row for lca-support, describing the number of proteins/spectra assigned to the respective LCA. Also the summary rule is adjusted for csv export, we only have to adjust the separator and includes spectra in output (if available). The lca rule is changed and in the new tools folder is the script for determining lca on existing summary files.

Edited by Juliane Schmachtenberg

Merge request reports