python/pymethylprocess/PreProcessDataTypes.py
def download_clinical(self, output_dir):
        """Download TCGA Clinical Data.

        Parameters
        ----------
        output_dir
            Where to output clinical data csv."""
        robjects.r("""
                   library(TCGAbiolinks)
                   library(data.table)
                   projects <- TCGAbiolinks:::getGDCprojects()$project_id
                   projects <- projects[grepl('^TCGA',projects,perl=T)]
                   match.file.cases.all <- NULL
                   data <- list()
                   for(n in 1:length(projects)){
                        proj <- projects[n]
                        clin.query <- GDCquery_clinic(project = proj,
                                          type='clinical', save.csv=F)
                        data[[length(data)+1]] = clin.query
                    }
                    df <- rbindlist(data)
                    write.csv(df, file=file.path('%s','clinical_info.csv'))
                   """%output_dir)
Download TCGA Clinical Data.

        Parameters
        ----------
        output_dir
            Where to output clinical data csv.
Download TCGA Clinical Data.
Parameters

output_dir
Where to output clinical data csv.
Download TCGA Clinical Data . Parameters output_dir Where to output clinical data csv .
def download_clinical(self, output_dir):
        robjects.r("""
                   library(TCGAbiolinks)
                   library(data.table)
                   projects <- TCGAbiolinks:::getGDCprojects()$project_id
                   projects <- projects[grepl('^TCGA',projects,perl=T)]
                   match.file.cases.all <- NULL
                   data <- list()
                   for(n in 1:length(projects)){
                        proj <- projects[n]
                        clin.query <- GDCquery_clinic(project = proj,
                                          type='clinical', save.csv=F)
                        data[[length(data)+1]] = clin.query
                    }
                    df <- rbindlist(data)
                    write.csv(df, file=file.path('%s','clinical_info.csv'))
                   """%output_dir)
def download_clinical ( self , output_dir ) : robjects . r ( """
                   library(TCGAbiolinks)
                   library(data.table)
                   projects <- TCGAbiolinks:::getGDCprojects()$project_id
                   projects <- projects[grepl('^TCGA',projects,perl=T)]
                   match.file.cases.all <- NULL
                   data <- list()
                   for(n in 1:length(projects)){
                        proj <- projects[n]
                        clin.query <- GDCquery_clinic(project = proj,
                                          type='clinical', save.csv=F)
                        data[[length(data)+1]] = clin.query
                    }
                    df <- rbindlist(data)
                    write.csv(df, file=file.path('%s','clinical_info.csv'))
                   """ % output_dir )
Download TCGA Clinical Data.
Download TCGA Clinical Data .
"""Download TCGA Clinical Data.

        Parameters
        ----------
        output_dir
            Where to output clinical data csv."""
self
output_dir