vignettes/cBioPortalData.Rmd
cBioPortalData.RmdThis vignette lays out the two main user-facing functions for downloading and representing data from the cBioPortal API. cBioDataPack makes use of the legacy distribution data method in cBioPortal (via tarballs). cBioPortalData allows for a more flexibile approach to obtaining data based on several available parameters including available molecular profiles.
This function will access the packaged data from and return an integrative MultiAssayExperiment representation.
## Use ask=FALSE for non-interactive use cBioDataPack("laml_tcga", ask = FALSE)
## A MultiAssayExperiment object of 12 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 12:
## [1] cna_hg19.seg: RaggedExperiment with 13571 rows and 191 columns
## [2] CNA: SummarizedExperiment with 24776 rows and 191 columns
## [3] linear_CNA: SummarizedExperiment with 24776 rows and 191 columns
## [4] methylation_hm27: SummarizedExperiment with 10919 rows and 194 columns
## [5] methylation_hm450: SummarizedExperiment with 10919 rows and 194 columns
## [6] mutations_extended: RaggedExperiment with 2584 rows and 197 columns
## [7] mutations_mskcc: RaggedExperiment with 2584 rows and 197 columns
## [8] RNA_Seq_expression_median: SummarizedExperiment with 19720 rows and 179 columns
## [9] RNA_Seq_mRNA_median_all_sample_Zscores: SummarizedExperiment with 19720 rows and 179 columns
## [10] RNA_Seq_v2_expression_median: SummarizedExperiment with 20531 rows and 173 columns
## [11] RNA_Seq_v2_mRNA_median_all_sample_Zscores: SummarizedExperiment with 20531 rows and 173 columns
## [12] RNA_Seq_v2_mRNA_median_Zscores: SummarizedExperiment with 20440 rows and 173 columns
## Features:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DFrame
## sampleMap() - the sample availability DFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DFrame
## assays() - convert ExperimentList to a SimpleList of matricesThis function provides a more flexible and granular way to request a MultiAssayExperiment object from a study ID, molecular profile, gene panel, sample list.
cbio <- cBioPortal() acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "IMPACT341", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA") )
## harmonizing input:
## removing 1 colData rownames not in sampleMap 'primary'acc## A MultiAssayExperiment object of 2 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 2:
## [1] acc_tcga_rppa: SummarizedExperiment with 57 rows and 46 columns
## [2] acc_tcga_linear_CNA: SummarizedExperiment with 339 rows and 90 columns
## Features:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DFrame
## sampleMap() - the sample availability DFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DFrame
## assays() - convert ExperimentList to a SimpleList of matricesIn cases where a download is interrupted, the user may experience a corrupt cache. The user can clear the cache for a particular study by using the removeCache function. Note that this function only works for data downloaded through the cBioDataPack function.
removeCache("laml_tcga")
For users who wish to clear the entire cBioPortalData cache, it is recommended that they use:
unlink("~/.cache/cBioPortalData/")
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] cBioPortalData_2.0.10 MultiAssayExperiment_1.14.0
## [3] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
## [5] matrixStats_0.56.0 Biobase_2.48.0
## [7] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
## [9] IRanges_2.22.2 S4Vectors_0.26.1
## [11] BiocGenerics_0.34.0 AnVIL_1.0.3
## [13] dplyr_1.0.2 BiocStyle_2.16.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 fs_1.5.0
## [3] bit64_4.0.4 progress_1.2.2
## [5] httr_1.4.2 rprojroot_1.3-2
## [7] GenomicDataCommons_1.12.0 tools_4.0.0
## [9] backports_1.1.9 R6_2.4.1
## [11] DBI_1.1.0 tidyselect_1.1.0
## [13] prettyunits_1.1.1 TCGAutils_1.8.0
## [15] bit_4.0.4 curl_4.3
## [17] compiler_4.0.0 rvest_0.3.6
## [19] formatR_1.7 xml2_1.3.2
## [21] desc_1.2.0 rtracklayer_1.48.0
## [23] bookdown_0.20 readr_1.3.1
## [25] askpass_1.1 rappdirs_0.3.1
## [27] pkgdown_1.5.1 rapiclient_0.1.3
## [29] RCircos_1.2.1 stringr_1.4.0
## [31] digest_0.6.25 Rsamtools_2.4.0
## [33] rmarkdown_2.3 XVector_0.28.0
## [35] pkgconfig_2.0.3 htmltools_0.5.0
## [37] dbplyr_1.4.4 limma_3.44.3
## [39] rlang_0.4.7 RSQLite_2.2.0
## [41] generics_0.0.2 jsonlite_1.7.0
## [43] BiocParallel_1.22.0 RCurl_1.98-1.2
## [45] magrittr_1.5 GenomeInfoDbData_1.2.3
## [47] futile.logger_1.4.3 Matrix_1.2-18
## [49] Rcpp_1.0.5 lifecycle_0.2.0
## [51] stringi_1.4.6 yaml_2.2.1
## [53] RaggedExperiment_1.12.0 MASS_7.3-52
## [55] RJSONIO_1.3-1.4 zlibbioc_1.34.0
## [57] BiocFileCache_1.12.1 grid_4.0.0
## [59] blob_1.2.1 crayon_1.3.4
## [61] lattice_0.20-41 Biostrings_2.56.0
## [63] splines_4.0.0 GenomicFeatures_1.40.1
## [65] hms_0.5.3 knitr_1.29
## [67] pillar_1.4.6 codetools_0.2-16
## [69] biomaRt_2.44.1 futile.options_1.0.1
## [71] XML_3.99-0.5 glue_1.4.2
## [73] evaluate_0.14 lambda.r_1.2.4
## [75] data.table_1.13.0 BiocManager_1.30.10
## [77] vctrs_0.3.3 tidyr_1.1.2
## [79] openssl_1.4.2 purrr_0.3.4
## [81] assertthat_0.2.1 xfun_0.16
## [83] survival_3.2-3 tibble_3.0.3
## [85] RTCGAToolbox_2.18.0 GenomicAlignments_1.24.0
## [87] AnnotationDbi_1.50.3 memoise_1.1.0
## [89] ellipsis_0.3.1