buildPancanSE: helper for SummarizedExperiment construction from pancan

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

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,
  featIDMap = featIDMapper()
)

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'. 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

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
   }
}

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.