CombineScores is the last node of PheNoBo.
It is the successor of the GeneticNetworkScore node.
This node combines 2 results from the phenotype, metabotype and/or genotype analysis.
The aim of CombineScores is to unite 2 sets of gene scores into a single gene score for each gene.
The combined scores are used to rank the genes.
Genes with a low rank (appearing first in the list of genes) are likely to cause the patient's condition.
CombineScores requires 2 tables with gene scores.
For detailed information about the format of the tables have a look at the Input Port section and
at the example files provided at https://github.com/marie-sophie/mapra.
CombineScores calculates 2 different scores.
Combined Gene Score:
The combined gene score is a probability calculated from the scores of 2 different, independent analyses
yielding scores g1 and g2.
The combined score g is determined by using Bayes' formula:
g=g1g2/(g1g2+(1-g1)(1-g2)).
Enrichment score:
The probabilities are translated into enrichment scores to facilitate the interpretation of the results.
The enrichment score of a gene with probability g is determined as log10(gn) where n denotes the total number of genes.
If the enrichment score is greater than 0, the gene score is higher than expected for a random prediction (where all genes get a score of n-1).
If the enrichment score is lower than 0, the gene score is lower than expected for a random prediction.
The algorithm of CombineScores is derived from the Phen-Gen tool (see Javed et al., 2014) and is described in more detail at...
Input Ports
- Gene Scores 1: a table produced by the GeneticNetworkScore node, e.g. from the phenotype analysis. This node uses the columns gene_id and gene_probability.
- Gene Scores 2: a table produced by the GeneticNetworkScore node, e.g. from the metabotype analysis. This node uses the columns gene_id and gene_probability.
Output Ports
- Combined Scores: Each row represents a gene and consists of 3 columns: gene_id, gene_probability and enrichment_score. The column gene_probability contains the combined gene scores based on 2 independently calculated sets of gene scores (input port 0 and 1). The gene probability indicates the likelihood that the gene is causal for the patient's disease. The column enrichment_score is a gene score that is normalized for the total number of genes. If the enrichment score is above 0, the gene probability is higher than expected for a random prediction.
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