querymolecular: Query DisGeNET for given disease(s) and generates an...

In aGutierrezSacristan/comorbidity: Analyze comorbidities from electronic health record data

Description

Given a file with diseases, a comorbidity analysis is perform according to the genes shared between the diseases. The comorbidity analysis can be performed at cui level or in a higher category specified in the input file. It generates a molecularComorbidity object.

Usage

querymolecular(filePth, unify = FALSE, database = "CURATED",
  score = c(0, 1), verbose = FALSE, warnings = TRUE)

Arguments

filePth	The file name and with the complete path where the file with disorders of interest is located
unify	By default it is set to FALSE. If the argument is set to TRUE, the name colum from the cui disease file will be selected for doing the comorbidity analysis.
database	Name of the database that will be queried. It can take the values 'CTD_human' to use Comparative Toxicogenomics Database, human data; 'UNIPROT' to use Universal Protein Resource;'CLINVAR' to use ClinVar, a public archive of relationships among sequence variation and human phenotype; 'GWASCAT' to use the NHGRI-EBI GWAS Catalog; 'ORPHANET', to use Orphanet, the portal for rare diseases and orphan drugs; 'CURATED' to use expert curated, human databases; 'RGD', to use Rat Genome Database; 'MGD', to use the Mouse Genome Database; 'CTD_rat' to use Comparative Toxicogenomics Database, rat data; 'CTD_mouse' to use Comparative Toxicogenomics Database, mouse data; 'PREDICTED' to use the expert curated, animal models data; 'ALL' to use all these databases. Default 'CURATED'.
score	A vector with two elements: 1) minimum score; 2) the maximum score. By default it is set to c(0, 1). It means that all the data available in DisGeNET will be used for the comorbidity analysis.
verbose	By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings	By default TRUE. Change it to FALSE to don't see the warnings.

Value

An object of class molecularComorbidity

Examples

ex1 <- querymolecular(
              filePth = system.file("extdata", "cuiDiseaseList.txt", package="comoRbidity"),
              unify    = TRUE,
              verbose  = FALSE
              )

aGutierrezSacristan/comorbidity documentation built on April 10, 2020, 5:54 p.m.