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Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
waldronlab/cBioPortalData
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ThecBioPortalData R package aims to import cBioPortal datasets asMultiAssayExperimentobjects into Bioconductor. Some of the features of the package include:
- The use of the
MultiAssayExperimentintegrative container forcoordinating and representing the data. - The data container explicitly links all assays to the patientclinical/pathological data.
- With aflexibleAPI,
MultiAssayExperimentprovides harmonized subsetting and reshapinginto convenient wide and long formats. - The package provides datasets from both the API and the savedpackaged data.
- It also provides automatic local caching, thanks toBiocFileCache
To install from Bioconductor (recommended for most users, this willinstall the release or development version corresponding to your versionof Bioconductor):
if (!require("BiocManager",quietly=TRUE)) install.packages("BiocManager")BiocManager::install("cBioPortalData")
Developers may want to install from GitHub for bleeding-edge updates(although this is generally not necessary because changes here are alsopushed tobioc-devel).Note that developers must be working with the development version ofBioconductor; seebioc-devel fordetails.
if (!require("cBioPortalData",quietly=TRUE))BiocManager::install("waldronlab/cBioPortalData")
To load the package:
library(cBioPortalData)cBioPortalData is a work in progress due to changes in data curationand cBioPortal API specification. Users can view thedata(studiesTable) dataset to get an overview of the studies that areavailable and currently building asMultiAssayExperimentrepresentations. About 89 % of the studies via the API (api_build) and93 % of the package studies (pack_build) are building, these includeadditional datasets that were not previously available. Feel free tofile an issue to request prioritization of fixing any of the remainingdatasets.
cbio<- cBioPortal()studies<- getStudies(cbio,buildReport=TRUE)
table(studies$api_build)#>#> FALSE TRUE#> 40 340table(studies$pack_build)#>#> FALSE TRUE#> 28 352
Flexible and granular access to cBioPortal data fromcbioportal.org/api. This option is best used with a particular genepanel of interest. It allows users to download sections of the data withmolecular profile and gene panel combinations within a study.
gbm<- cBioPortalData(api=cbio,by="hugoGeneSymbol",studyId="gbm_tcga",genePanelId="IMPACT341",molecularProfileIds= c("gbm_tcga_rppa","gbm_tcga_mrna"))
gbm#> A MultiAssayExperiment object of 2 listed#> experiments with user-defined names and respective classes.#> Containing an ExperimentList class object of length 2:#> [1] gbm_tcga_mrna: SummarizedExperiment with 336 rows and 401 columns#> [2] gbm_tcga_rppa: SummarizedExperiment with 67 rows and 244 columns#> Functionality:#> experiments() - obtain the ExperimentList instance#> colData() - the primary/phenotype DataFrame#> sampleMap() - the sample coordination DataFrame#> `$`, `[`, `[[` - extract colData columns, subset, or experiment#> *Format() - convert into a long or wide DataFrame#> assays() - convert ExperimentList to a SimpleList of matrices#> exportClass() - save data to flat files
This function will download a dataset from thecbioportal.org/datasetswebsite as a packaged tarball and serve it to users as aMultiAssayExperiment object. This option is good for users who areinterested in obtaining all the data for a particular study.
acc<- cBioDataPack("acc_tcga")
acc#> A MultiAssayExperiment object of 10 listed#> experiments with user-defined names and respective classes.#> Containing an ExperimentList class object of length 10:#> [1] cna_hg19.seg: RaggedExperiment with 16080 rows and 90 columns#> [2] cna: SummarizedExperiment with 24776 rows and 90 columns#> [3] linear_cna: SummarizedExperiment with 24776 rows and 90 columns#> [4] methylation_hm450: SummarizedExperiment with 15754 rows and 80 columns#> [5] mrna_seq_v2_rsem_zscores_ref_all_samples: SummarizedExperiment with 20531 rows and 79 columns#> [6] mrna_seq_v2_rsem_zscores_ref_diploid_samples: SummarizedExperiment with 20440 rows and 79 columns#> [7] mrna_seq_v2_rsem: SummarizedExperiment with 20531 rows and 79 columns#> [8] mutations: RaggedExperiment with 20166 rows and 90 columns#> [9] rppa_zscores: SummarizedExperiment with 191 rows and 46 columns#> [10] rppa: SummarizedExperiment with 192 rows and 46 columns#> Functionality:#> experiments() - obtain the ExperimentList instance#> colData() - the primary/phenotype DataFrame#> sampleMap() - the sample coordination DataFrame#> `$`, `[`, `[[` - extract colData columns, subset, or experiment#> *Format() - convert into a long or wide DataFrame#> assays() - convert ExperimentList to a SimpleList of matrices#> exportClass() - save data to flat files
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Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
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