brcaMAE: a virtual MultiAssayExperiment for pancancer-atlas BRCA data

In BiocOncoTK: Bioconductor components for general cancer genomics

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

BiocOncoTK documentation built on Nov. 8, 2020, 6:03 p.m.