buildPancanSE {BiocOncoTK} | R Documentation

## helper for SummarizedExperiment construction from pancan

### Description

helper for SummarizedExperiment construction from pancan

### Usage

    buildPancanSE(bq, acronym = "BLCA", assay = "meth450k",
      sampType = "TP", subjectIDName = "ParticipantBarcode",
      seTransform = force, bindMethRowranges = TRUE)

### Arguments

`bq` | instance of BigQueryConnection for pancancer-atlas.Annotated Dataset
`acronym` | character(1) 'cohort' label, e.g., 'BLCA'
`assay` | character(1) element from names(BiocOncoTK::annotTabs), e.g., 'meth450k'
`sampType` | character(1) element from BiocOncoTK::pancan_sampTypeMap$"SampleTypeLetterCode", e.g., 'TP' for Primary solid Tumor samples, or 'TB' for peripheral blood sample from primary blood derived cancer
`subjectIDName` | character(1) field name for subject identifier
`seTransform` | a function that accepts a SummarizedExperiment and returns a SummarizedExperiment; useful for feature name remapping, defaults to force (does nothing)
`bindMethRowranges` | logical(1) if true and assay is meth27k or meth450k, annotation from FDb.InfiniumMethylation.hg19 and EnsDb.Hsapiens.v75 is obtained for available features and bound into the rowRanges component of returned object

### Value

SummarizedExperiment, with metadata on acronym, assay, and sampleType propagated; if the assay is a methylation assay and bindMethRowranges is TRUE, a RangedSummarizedExperiment is returned.

### Note

Note that pancancer-atlas is distinguished from TCGA by the presence of more sample types. The default type is 'TP' for primary solid tumor. Codes and their interpretations are available in BiocOncoTK::pancan_sampTypeMap.

### Examples

    if (interactive() && Biobase::testBioCConnection()) {
       billco = Sys.getenv("CGC_BILLING")
       if (nchar(billco)>0) {
         bq = pancan_BQ()
         methSE_BLCA = try(buildPancanSE(bq))
         methSE_BLCA
       }
    }

[Package BiocOncoTK version 1.2.1 Index]