brcaMAE {BiocOncoTK} | R Documentation

## a virtual MultiAssayExperiment for pancancer-atlas BRCA data

### Description

a virtual MultiAssayExperiment for pancancer-atlas BRCA data

### Usage

    brcaMAE

### Format

MultiAssayExperiment instance with DelayedArray (BQ3_Array) assay data

### Note

Constructed as

    library(BiocOncoTK)
    pcbq = pancan_BQ()
    library(restfulSE)
    BRCA_mir = pancan_SE(pcbq)
    BRCA_mrna = pancan_SE(pcbq,
       assayDataTableName = pancan_longname("rnaseq"),
       assayFeatureName = "Entrez",
       assayValueFieldName = "normalized_count")
    BRCA_rppa = pancan_SE(pcbq,
       assayDataTableName = pancan_longname("RPPA"),
       assayFeatureName = "Protein",
       assayValueFieldName = "Value")
    BRCA_meth = pancan_SE(pcbq,
       assayDataTableName = pancan_longname("27k")[2],
       assayFeatureName = "ID",
       assayValueFieldName = "Beta")
    library(MultiAssayExperiment)
    library(dplyr)
    library(magrittr)
    clinBRCA = pcbq %>% tbl(pancan_longname("clinical")) %>%
      filter(acronym=="BRCA") %>% as.data.frame()
    rownames(clinBRCA) = clinBRCA[,2]
    clinDF = DataFrame(clinBRCA)
    library(MultiAssayExperiment)
    brcaMAE = MultiAssayExperiment(
      ExperimentList(rnaseq=BRCA_mrna, meth=BRCA_meth, rppa=BRCA_rppa,
        mirna=BRCA_mir),colData=clinDF)
    upsetSamples(brcaMAE) # to view display

### Source

ISB BigQuery pancan-atlas project

### Examples

    if (requireNamespace("MultiAssayExperiment"))
    BiocOncoTK::brcaMAE

[Package BiocOncoTK version 1.4.0 Index]