seByTumor_2016 {restfulSE} | R Documentation |
Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
seByTumor_2016(tumorCode = "LUAD", assayTblName = "mRNA_UNC_HiSeq_RSEM", rdColsToKeep = c("original_gene_symbol", "HGNC_gene_symbol", "gene_id", "Study"), bqConn)
tumorCode |
one of the concise TCGA codes in a character string – not checked, defaults to "LUAD", lung adenocarcinoma |
assayTblName |
the name of the assay whose annotation will be used as rowData |
rdColsToKeep |
columns of assay table to use in rowData component |
bqConn |
instance of BigQueryConnection from bigrquery |
SummarizedExperiment instance, with BigQuery reference as assay