output_gene_prioritization: Retrieve genes related to a disease query
In jeinson/PhenolyzerR: PhenolyzerR

Description Usage Arguments Details Examples

View source: R/output_gene_prioritization.R

This function calls disease_extension to perform a descendant search, then prioritizes the disease terms matched to the disease-gene databases using system described in the paper.

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output_gene_prioritization(disease_term, ontologies = c("ctd", "doid"),
  output_mode = "aggregate", return_output = TRUE, wordcloud = FALSE,
  predict = FALSE)

`disease_term`	A disease for which to find related genes
`ontologies`	Defaults to c("ctd", "doid").
`output_mode`	Specifies if the output is a table of genes, or a list of tibbles with individual genes and source information
`return_output`	Logical. Specify if the output should be returned. Useful if you only want a wordcloud.

In brief, each database has its own quality metrics. These are given an ad hoc score, and matches are weighted based on this score. The prioritized list is ordered, and normalized by diving through all scores by the max score.