buildPancanSE {BiocOncoTK} | R Documentation |
helper for SummarizedExperiment construction from pancan
buildPancanSE(bq, acronym = "BLCA", assay = "meth450k", sampType = "TP", subjectIDName = "ParticipantBarcode", seTransform = force, bindMethRowranges = TRUE)
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 |
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 } }