# psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

## Documentation for package ‘psygenet2r’ version 1.22.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DataGeNET.Psy-class | Class DataGeNET.Psy
DataGeNET.Psy-plot | Plots the content of a 'DataGeNET.Psy' object
enrichedPD | Enrichment of a user's input (genes) in PsyGeNET's diseases.
extract | Raw data from 'DataGeNET.Psy' and 'JaccardIndexPsy'.
extract-method | Raw data from 'DataGeNET.Psy' and 'JaccardIndexPsy'.
extractSentences | Method to obtain the sentences that support a gene-disease association from a 'DataGeNET.Psy' object.
extractSentences-method | Method to obtain the sentences that support a gene-disease association from a 'DataGeNET.Psy' object.
geneAttrPlot | Ploting the relation between genes and disease-categories
getUMLs | Query PsyGeNET for given gene(s) and generates an 'DataGeNET.Psy'
jaccardEstimation | Calculation of the Jaccard Index between ideseases
JaccardIndexPsy-class | Class JaccardIndexPsy
JaccardIndexPsy-plot | Plot the content of a 'JaccardIndexPsy' object.
ndisease | Getter from 'DataGeNET.Psy'.
ndisease-method | Getter from 'DataGeNET.Psy'.
ngene | Getter from 'DataGeNET.Psy'.
ngene-method | Getter from 'DataGeNET.Psy'.
pantherGraphic | Query PsyGeNET for given genes and creates a representation in base of their panther-class
plot-method | Plots the content of a 'DataGeNET.Psy' object
plot-method | Plot the content of a 'JaccardIndexPsy' object.
psygenet2r | psygenet2r: Package to query PsyGeNET database and to perform comorbidity studies
psygenetDisease | Query PsyGeNET for given disease(s) and generates an 'DataGeNET.Psy'
psygenetDiseaseSentences | Query PsyGeNET for given disease(s) and extract the pmids sentences that report a gene-disease asssociation.
psygenetGene | Query PsyGeNET for given gene(s) and generates an 'DataGeNET.Psy'
psygenetGeneSentences | Query PsyGeNET for given gene(s) and extract the pmids sentences that report a gene-disease asssociation.
qr | 'DataGeNET.Psy' obtained from quering PsyGeNET for gene '4852'.
topAnatEnrichment | Enrichment of a user's input (genes) in anatomical terms (TopAnat).
universe | Vector with gene universe for Jaccard Index