pancan_SE {restfulSE} | R Documentation |
illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment
pancan_SE(bqcon, colDataTableName = "clinical_PANCAN_patient_with_followup", colDSubjectIdName = "bcr_patient_barcode", colDFilterField = "acronym", colDFilterValue = "BRCA", assayDataTableName = "pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16_annot", assayFeatureName = "ID", subjectIDName = "ParticipantBarcode", tumorFieldName = "Study", tumorFieldValue = "BRCA", assayValueFieldName = "miRNAexpr")
bqcon |
a BigQueryConnection instance |
colDataTableName |
character(1) defaulting to "clinical_PANCAN_patient_with_followup" |
colDSubjectIdName |
character(1) defaulting to "bcr_patient_barcode" |
colDFilterField |
character(1) defaulting to "acronym" |
colDFilterValue |
character(1) defaulting to "BRCA" |
assayDataTableName |
character(1) defaulting to "pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16_annot" |
assayFeatureName |
character(1) defaulting to "ID" |
subjectIDName |
character(1) defaulting to "ParticipantBarcode" |
tumorFieldName |
character(1) defaulting to "Study" |
tumorFieldValue |
character(1) defaulting to "BRCA" |
assayValueFieldName |
character(1) defaulting to "miRNAexpr" |
an instance of SummarizedExperiment
The parameters need different assignments for different tables. Field names are not standardized across tables.
if (interactive() & requireNamespace("DBI") & requireNamespace("bigrquery")) { pancan_BQ_loc = function (dataset="Annotated", billing=Sys.getenv("CGC_BILLING")) { con <- DBI::dbConnect(bigrquery::dbi_driver(), project = "pancancer-atlas", dataset = dataset, billing = billing) con } bqcon = try(pancan_BQ_loc()) # needs CGC_BILLING in environment if (!inherits(bqcon, "try-error")) pancan_SE(bqcon) }