seByTumor_2016: Given a BigQueryConnection to the 2016 ISB TCGA bigtables,...
In restfulSE: Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Description
Usage
Arguments
Value
Description
Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
Usage
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seByTumor_2016(
tumorCode = "LUAD",
assayTblName = "mRNA_UNC_HiSeq_RSEM",
rdColsToKeep = c("original_gene_symbol", "HGNC_gene_symbol", "gene_id", "Study"),
bqConn
)
Arguments
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
Value
SummarizedExperiment instance, with BigQuery reference as assay
restfulSE documentation built on Nov. 8, 2020, 8:01 p.m.
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Description Usage Arguments Value
Description
Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
Usage
1 2 3 4 5 6 | seByTumor_2016(
tumorCode = "LUAD",
assayTblName = "mRNA_UNC_HiSeq_RSEM",
rdColsToKeep = c("original_gene_symbol", "HGNC_gene_symbol", "gene_id", "Study"),
bqConn
)
|
Arguments
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 |
Value
SummarizedExperiment instance, with BigQuery reference as assay
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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