# an R package to query, visualize, and expand DisGeNET data

## Documentation for package ‘disgenet2r’ version 0.99.3

- DESCRIPTION file.

## Help Pages

DataGeNET.DGN-class | Class DataGeNET.DGN
DataGeNET.DGN-methods | Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
DataGeNET.DGN-methods | Obtain the number of unique diseases in a 'DataGeNET.DGN'.
DataGeNET.DGN-methods | Obtain the number of unique genes in a 'DataGeNET.DGN'.
DataGeNET.DGN-methods | Plots the content of a 'DataGeNET.DGN' object. This functions allows to create a variety of plots for 'DataGeNET.DGN' objects.
DataGeNET.Dis-methods | Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
DataGeNET.RDF-class | Class DataGeNET.RDF
disease2attribute | Retrieves genes associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease2biologicalprocess | Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2cellcomponent | Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2compound | Query for given disease(s) and generates an 'DataGeNET.RDF'
disease2disease_by_gene | Retrieves disease-disease associations via shared genes and generates an 'DataGeNET.DGN'
disease2disease_by_variant | Retrieves disease-disease associations via shared genes and generates an 'DataGeNET.DGN'
disease2evidence | Retrieves evidences supporting the associations, for a disease, or a list of diseases, and generates an 'DataGeNET.DGN'
disease2gene | Retrieves genes associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease2molecularfunction | Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2pathway | Query for given disease(s) and generates an 'DataGeNET.RDF'
disease2variant | Retrieves variants associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease_enrichment | Performs an enrichment analysis on a list of genes/variants and generates an object 'DataGeNET.DGN'
extract | Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
gene2biologicalprocess | Query for given gene(s) and generates an 'DataGeNET.RDF'
gene2cellcomponent | Query for given gene(s) and generates an 'DataGeNET.RDF'
gene2disease | Retrieves diseases associated to a gene, or list of genes and generates an 'DataGeNET.DGN'
gene2evidence | Retrieves evidences supporting a gene-disease association, for a gene, or list of genes and generates an 'DataGeNET.DGN'
gene2indication | Query for given gene(s) and generates an 'DataGeNET.RDF' Given the NCBI gene identifier, retrieves the information related to drugs which interacts with the gene product and their indications and creates an object of type 'DataGeNET.RDF'.
gene2molecularfunction | Query for given gene(s) and generates an 'DataGeNET.RDF'
get_disgenet_api_key | Retrieves the DisGeNET API key for a user
get_disgenet_version | Retrieves DisGeNET data version
get_similar_diseases | Retrieves diseases similar to an input disease and generates an 'DataGeNET.DGN'
get_umls_from_vocabulary | Retrieves mappings from different vocabularies associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
ndisease | Obtain the number of unique diseases in a 'DataGeNET.DGN'.
ngene | Obtain the number of unique genes in a 'DataGeNET.DGN'.
pathway2disease | Query for given pathway(s) and generates an 'DataGeNET.RDF'
plot | Plots the content of a 'DataGeNET.DGN' object. This functions allows to create a variety of plots for 'DataGeNET.DGN' objects.
pvalue_estimation | Estimates the p value of the Jaccard Coefficient for pairs of diseases
variant2disease | Retrieves diseases associated to a variant or list of variants and generates an 'DataGeNET.DGN'
variant2evidence | Retrieves evidences supporting a gene-disease association, for a gene, or list of genes and generates an 'DataGeNET.DGN'