Contents

Installation

library(cBioPortalData)
library(AnVIL)
library(rapiclient)

Two main interfaces

cBioDataPack: Obtain Study Data as Zipped Tarballs

This function will access the packaged data from and return an integrative MultiAssayExperiment representation.

cBioDataPack("laml_tcga")
## A MultiAssayExperiment object of 11 listed
##  experiments with user-defined names and respective classes. 
##  Containing an ExperimentList class object of length 11: 
##  [1] CNA: SummarizedExperiment with 24776 rows and 191 columns 
##  [2] RNA_Seq_expression_median: SummarizedExperiment with 19720 rows and 179 columns 
##  [3] RNA_Seq_mRNA_median_Zscores: SummarizedExperiment with 19720 rows and 179 columns 
##  [4] RNA_Seq_v2_expression_median: SummarizedExperiment with 20531 rows and 173 columns 
##  [5] RNA_Seq_v2_mRNA_median_Zscores: SummarizedExperiment with 20531 rows and 173 columns 
##  [6] cna_hg19.seg: RaggedExperiment with 13571 rows and 191 columns 
##  [7] linear_CNA: SummarizedExperiment with 24776 rows and 191 columns 
##  [8] methylation_hm27: SummarizedExperiment with 10924 rows and 194 columns 
##  [9] methylation_hm450: SummarizedExperiment with 10924 rows and 194 columns 
##  [10] mutations_extended: RaggedExperiment with 2584 rows and 197 columns 
##  [11] mutations_mskcc: RaggedExperiment with 2584 rows and 197 columns 
## Features: 
##  experiments() - obtain the ExperimentList instance 
##  colData() - the primary/phenotype DFrame 
##  sampleMap() - the sample availability DFrame 
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment 
##  *Format() - convert into a long or wide DFrame 
##  assays() - convert ExperimentList to a SimpleList of matrices

cBioPortalData: Obtain data from the cBioPortal API

This function provides a more flexible and granular way to request a MultiAssayExperiment object from a study ID, molecular profile, gene panel, sample list.

cbio <- cBioPortal()
acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga",
    genePanelId = "IMPACT341",
    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
)
## harmonizing input:
##   removing 1 colData rownames not in sampleMap 'primary'
acc
## A MultiAssayExperiment object of 2 listed
##  experiments with user-defined names and respective classes. 
##  Containing an ExperimentList class object of length 2: 
##  [1] acc_tcga_rppa: SummarizedExperiment with 57 rows and 46 columns 
##  [2] acc_tcga_linear_CNA: SummarizedExperiment with 339 rows and 90 columns 
## Features: 
##  experiments() - obtain the ExperimentList instance 
##  colData() - the primary/phenotype DFrame 
##  sampleMap() - the sample availability DFrame 
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment 
##  *Format() - convert into a long or wide DFrame 
##  assays() - convert ExperimentList to a SimpleList of matrices