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File NAMESPACE Modified

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 # Generated by roxygen2: do not edit by hand
 
-export(disease2compound)
-export(disease2pathway)
-export(disease2phenotype)
 export(disease2variant)
 export(diseaseMapping)
 export(disgenetDisDis)
 export(disgenetDisease)
 export(disgenetGene)
-export(gene2biologicalprocess)
-export(gene2cellcomponent)
-export(gene2indication)
-export(gene2molecularfunction)
 export(getUMLs)
 export(pValueEstimation)
-export(pathway2disease)
-export(phenotype2disease)
 export(plot)
 export(variant2disease)
 exportClasses(DataGeNET.DGN)

File R/disease2compound.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' dis2com <- disease2compound( disease = "C3542021", database = "ALL" )
-#' @export disease2compound
+### @export disease2compound
 
 
 disease2compound <- function( disease = "C3542021", database = "CURATED", score = c(">", 0), verbose = FALSE, warnings = TRUE ) {

File R/disease2pathway.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' dis2path <- disease2pathway( disease = "C0751955" )
-#' @export disease2pathway
+### @export disease2pathway
 
 
 disease2pathway <- function( disease , database = "CURATED", score = c(">", 0), verbose = FALSE, warnings = TRUE ) {

File R/figurasVarias.R Deleted

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Empty file removed.

File R/gene2biologicalprocess.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' gene2bp <- gene2biologicalprocess( gene = 1588 )
-#' @export gene2biologicalprocess
+## @export gene2biologicalprocess
 
 
 #gene2biologicalprocess <- function( gene, database = "CURATED", score = c(">", 0), verbose = FALSE, warnings = TRUE ) {

File R/gene2cellcomponent.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' gene2cc <- gene2cellcomponent( gene = 1588 )
-#' @export gene2cellcomponent
+## @export gene2cellcomponent
 
 
 gene2cellcomponent <- function( gene, verbose = FALSE, warnings = TRUE ) {

File R/gene2indication.R Modified

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 # @return An object of class \code{DataGeNET.RDF}
 # @examples
 # gene2indi <- gene2indication( gene = 1588 )
-#' @export gene2indication
+## @export gene2indication
 
 
 gene2indication <- function( gene,  verbose = FALSE, warnings = TRUE ) {

File R/gene2molecularfunction.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' gene2mf <- gene2molecularfunction( gene = 1588 )
-#' @export gene2molecularfunction
+## @export gene2molecularfunction
 
 
 #gene2molecularfunction <- function( gene, database = "CURATED", score = c(">", 0), verbose = FALSE, warnings = TRUE ) {

File R/pathway2disease.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' path2dis <- pathway2disease( pathway = "WP1545" )
-#' @export pathway2disease
+## @export pathway2disease
 
 
 pathway2disease <-  function(pathway ,   database = "CURATED",    score = c(">", 0), verbose = FALSE, warnings = TRUE) {

File R/phenotype2disease.R Modified

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 #' @return An object of class \code{DataGeNET.RDF}
 #' @examples
 #' pheno2dis <- phenotype2disease( phenotypeID = "0000316" )
-#' @export phenotype2disease
+## @export phenotype2disease
 
 
 phenotype2disease <- function( phenotypeID = "0000316" , verbose = FALSE, warnings = FALSE ) {

File man/pValueEstimation.Rd Modified

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   verbose = FALSE)
 }
 \arguments{
-\item{database}{Name of the database that will be queried. It can take the values \code{'CTD_human'} to use Comparative
-Toxicogenomics Database, human data; \code{'UNIPROT'} to use Universal
-Protein Resource;\code{'CLINVAR'} to use ClinVar, a public archive of relationships
-among sequence variation and human phenotype; \code{'GWASCAT'} to use
-the NHGRI-EBI GWAS Catalog; \code{'ORPHANET'}, to use
-Orphanet, the portal for rare diseases and orphan drugs;
+\item{database}{Name of the database that will be queried. It can take the values:
+\code{'CTD_human'} to use Comparative Toxicogenomics Database, human data;
+\code{'UNIPROT'} to use Universal Protein Resource;
+\code{'CLINVAR'} to use ClinVar, a public archive of relationships
+among sequence variation and human phenotype;
+\code{'GWASCAT'} to use the NHGRI-EBI GWAS Catalog;
+\code{'ORPHANET'}, to use Orphanet, the portal for rare diseases and orphan drugs;
+\code{'PSYGENET'} to use PSYGENET;
+\code{'HPO'} to use HPO;
 \code{'CURATED'} to use expert curated, human databases;
-\code{'RGD'}, to use Rat Genome Database; \code{'MGD'}, to use the Mouse Genome Database;
 \code{'CTD_rat'} to use Comparative Toxicogenomics Database, rat data;
 \code{'CTD_mouse'} to use Comparative Toxicogenomics Database, mouse data;
-\code{'PREDICTED'} to use the expert curated, animal models data;
+\code{'RGD'}, to use Rat Genome Database;
+\code{'MGD'}, to use the Mouse Genome Database;
+\code{'ANIMAL_MODELS'} to use the expert curated, animal models data;
 \code{'ALL'} to use all these databases. Default \code{'CURATED'}.}
 
 \item{nboot}{Number of iterations sued to compute the pvalue associted