Calculate keynodes ranks (analysis)

Analysis title

Calculate keynodes ranks

Provider

Biosoft

Class

GEKnRankCalculator

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

This method takes the result of keynode analysis with additional column of gene identifiers. It adds optional score columns from three other tables called Transcriptome, Proteome and CMA score table. Any table of gene identifiers with numerical score column can be set as any of these three tables.

The result is ranked via the Keynodes Score column and via the newly added scores. The ranking procedure used is the following: molecules are sorted in descending order of scores and then integer numbers starting from 1 are assigned to each molecule. Molecules with the same score obtain the same rank number. The Total Rank is the sum of score-specific ranks for each molecule.

Parameters:

• Keynodes result – Path to table with keynodes result
• Column with gene IDs – Column with gene IDs
• Transcriptome – Path to transcriptome data table
• Optional transcriptome – Use transcriptomics score if present and skip if not present
• Score column (transcriptome) – Score column (transcriptome)
• Proteome – Path to proteome data table
• Score column (proteome) – Score column (proteome)
• CMA score table – Path to table with CMA model scores calculated (e.g. Model visualization table from CMA result)
• Result – Path to result table