buildPancanSE: helper for SummarizedExperiment construction from pancan
In BiocOncoTK: Bioconductor components for general cancer genomics

Description Usage Arguments Value Note Examples

helper for SummarizedExperiment construction from pancan

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

`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'. If 'assay == "mc3_MAF"' an error is thrown as the mutation data are inconsistently annotated; the message produced directs the user to 'mc3toGR'.
`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
`featIDMap`	a named character() vector defining, for each assay type, what field should be used to label features in rownames. 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

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 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.

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