R/psyGenDisId.R

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

psyGenDisId <- function( database, genDis ) {
    oql <- "DEFINE
    c0='/data/main',
    c1='/data/genes',
    c2='/data/diseases',
    c3='/data/datasources'
    ON
    'http://www.psygenet.org/web/PsyGeNET'
    SELECT
    c1 (Gene_Symbol, Gene_Id),
    c2 ( Disease_code, DiseaseName, PsychiatricDisorder),
    c0 (Disease_Id)
    FROM
    c0
    WHERE
    c3 = 'DB'
    ORDER BY
    c0.Score DESC" 
    
    oql <- stringr::str_replace(
        string      = oql,
        pattern     = "DB",
        replacement = database 
    )
    
    dataTsv <- download_data(oql)
    data <- read.csv( textConnection( dataTsv ), header = TRUE, sep="\t" ) 
    
    if ( genDis == "Gene" ){
        genes <- data[!duplicated(data[,1]),]
        genes <- genes[,c(1,2)]
        return ( genes )
    }
    if ( genDis == "Diseases" ){
        diseases <- data[!duplicated( data[,4] ),]
        diseases <- diseases[,c(6,3,4)]
        return( diseases )
    }
}