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 13 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 13:
## [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_mRNA_median_Zscores: SummarizedExperiment with 19719 rows and 179 columns
## [11] RNA_Seq_v2_expression_median: SummarizedExperiment with 20531 rows and 173 columns
## [12] RNA_Seq_v2_mRNA_median_all_sample_Zscores: SummarizedExperiment with 20531 rows and 173 columns
## [13] RNA_Seq_v2_mRNA_median_Zscores: SummarizedExperiment with 20440 rows and 173 columns
## Functionality:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DataFrame
## sampleMap() - the sample coordination DataFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DataFrame
## assays() - convert ExperimentList to a SimpleList of matrices
## exportClass() - save all data to filesThis function provides a more flexible and granular way to request a MultiAssayExperiment object from a study ID, molecular profile, gene panel, sample list.
cbio <- cBioPortal()
acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga",
genePanelId = "IMPACT341",
molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
)## harmonizing input:
## removing 1 colData rownames not in sampleMap 'primary'
acc## A MultiAssayExperiment object of 2 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 2:
## [1] acc_tcga_rppa: SummarizedExperiment with 57 rows and 46 columns
## [2] acc_tcga_linear_CNA: SummarizedExperiment with 339 rows and 90 columns
## Functionality:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DataFrame
## sampleMap() - the sample coordination DataFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DataFrame
## assays() - convert ExperimentList to a SimpleList of matrices
## exportClass() - save all data to filesIn 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 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.1 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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_2.2.6 MultiAssayExperiment_1.16.0
## [3] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [5] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
## [7] IRanges_2.24.1 S4Vectors_0.28.1
## [9] BiocGenerics_0.36.0 MatrixGenerics_1.2.0
## [11] matrixStats_0.57.0 AnVIL_1.2.0
## [13] dplyr_1.0.3 BiocStyle_2.18.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 fs_1.5.0
## [3] bit64_4.0.5 progress_1.2.2
## [5] httr_1.4.2 rprojroot_2.0.2
## [7] GenomicDataCommons_1.14.0 tools_4.0.3
## [9] R6_2.5.0 DBI_1.1.1
## [11] withr_2.4.0 tidyselect_1.1.0
## [13] prettyunits_1.1.1 TCGAutils_1.10.0
## [15] bit_4.0.4 curl_4.3
## [17] compiler_4.0.3 cli_2.2.0
## [19] rvest_0.3.6 textshaping_0.2.1
## [21] formatR_1.7 xml2_1.3.2
## [23] desc_1.2.0 DelayedArray_0.16.0
## [25] rtracklayer_1.50.0 bookdown_0.21
## [27] readr_1.4.0 askpass_1.1
## [29] rappdirs_0.3.1 pkgdown_1.6.1
## [31] rapiclient_0.1.3 RCircos_1.2.1
## [33] Rsamtools_2.6.0 systemfonts_0.3.2
## [35] stringr_1.4.0 digest_0.6.27
## [37] rmarkdown_2.6 XVector_0.30.0
## [39] pkgconfig_2.0.3 htmltools_0.5.1
## [41] dbplyr_2.0.0 limma_3.46.0
## [43] rlang_0.4.10 rstudioapi_0.13
## [45] RSQLite_2.2.2 generics_0.1.0
## [47] jsonlite_1.7.2 BiocParallel_1.24.1
## [49] RCurl_1.98-1.2 magrittr_2.0.1
## [51] GenomeInfoDbData_1.2.4 futile.logger_1.4.3
## [53] Matrix_1.3-2 fansi_0.4.2
## [55] Rcpp_1.0.6 lifecycle_0.2.0
## [57] stringi_1.5.3 yaml_2.2.1
## [59] RaggedExperiment_1.14.1 RJSONIO_1.3-1.4
## [61] zlibbioc_1.36.0 BiocFileCache_1.14.0
## [63] grid_4.0.3 blob_1.2.1
## [65] crayon_1.3.4 lattice_0.20-41
## [67] Biostrings_2.58.0 splines_4.0.3
## [69] GenomicFeatures_1.42.1 hms_1.0.0
## [71] ps_1.5.0 knitr_1.30
## [73] pillar_1.4.7 codetools_0.2-18
## [75] biomaRt_2.46.0 futile.options_1.0.1
## [77] XML_3.99-0.5 glue_1.4.2
## [79] evaluate_0.14 lambda.r_1.2.4
## [81] data.table_1.13.6 BiocManager_1.30.10
## [83] vctrs_0.3.6 tidyr_1.1.2
## [85] openssl_1.4.3 purrr_0.3.4
## [87] assertthat_0.2.1 xfun_0.20
## [89] ragg_0.4.1 survival_3.2-7
## [91] tibble_3.0.5 RTCGAToolbox_2.20.0
## [93] GenomicAlignments_1.26.0 AnnotationDbi_1.52.0
## [95] memoise_1.1.0 ellipsis_0.3.1