This function analyzes the file containing associations between ORPHAcodes and genes and saves them internally in an R-friendly format.
Usage
add_associated_genes(
filepath,
default = FALSE,
force = FALSE,
destdir = tools::R_user_dir("RDaggregator", "data")
)Arguments
- filepath
An xml file published by Orphanet containing the associations between ORPHAcodes and genes.
- default
If
TRUE, set the added association file as default.- force
If
TRUE, adds the association file even if an identical version was internally found.- destdir
The destination directory, in which the processed data will be saved.
Details
Orphanet publishes genes data on a 6-months basis, and is deployed in english only.
The different file versions are available here.
They must be downloaded locally to be added to RDaggregator.
As a gene mutation may have various effects on individuals health, this file indicates how genes and clinical entities are related, giving the association type and status. Genes can be referred through multiple referentials including HGNC, OMIM, Ensembl, Genatlas, Reactome and SwissProt.
The added file version will appear among the available options
through the RDaggregator_options() interface. It can also be manually set using the built-in
options() function and the "gene_file_version" name.