library(cBioPortalData)
library(AnVIL)This 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: SummarizedExperiment with 24776 rows and 191 columns
## [2] RNA_Seq_expression_median: SummarizedExperiment with 19720 rows and 179 columns
## [3] RNA_Seq_mRNA_median_all_sample_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 20440 rows and 173 columns
## [6] RNA_Seq_v2_mRNA_median_all_sample_Zscores: SummarizedExperiment with 20531 rows and 173 columns
## [7] cna_hg19.seg: RaggedExperiment with 13571 rows and 191 columns
## [8] linear_CNA: SummarizedExperiment with 24776 rows and 191 columns
## [9] methylation_hm27: SummarizedExperiment with 10919 rows and 194 columns
## [10] methylation_hm450: SummarizedExperiment with 10919 rows and 194 columns
## [11] mutations_extended: RaggedExperiment with 2584 rows and 197 columns
## [12] 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
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DFrame
## assays() - convert ExperimentList to a SimpleList of matricesThis function provides a more flexible and granular way to request a MultiAssayExperiment object from a study ID, molecular profile, gene panel, sample list.
cbio <- cBioPortal()
acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga",
genePanelId = "IMPACT341",
molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
)## harmonizing input:
## removing 1 colData rownames not in sampleMap 'primary'acc## A MultiAssayExperiment object of 2 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 2:
## [1] acc_tcga_rppa: SummarizedExperiment with 57 rows and 46 columns
## [2] acc_tcga_linear_CNA: SummarizedExperiment with 339 rows and 90 columns
## Features:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DFrame
## sampleMap() - the sample availability DFrame
## `$`, `[`, `[[` - 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/")sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server 2012 R2 x64 (build 9600)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## 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_0.57.0 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_2.16.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 bit64_4.0.5
## [3] progress_1.2.2 httr_1.4.2
## [5] GenomicDataCommons_1.12.0 tools_4.0.3
## [7] R6_2.4.1 DBI_1.1.0
## [9] tidyselect_1.1.0 prettyunits_1.1.1
## [11] TCGAutils_1.8.1 bit_4.0.4
## [13] curl_4.3 compiler_4.0.3
## [15] cli_2.1.0 rvest_0.3.6
## [17] formatR_1.7 xml2_1.3.2
## [19] rtracklayer_1.48.0 bookdown_0.21
## [21] readr_1.4.0 askpass_1.1
## [23] rappdirs_0.3.1 rapiclient_0.1.3
## [25] RCircos_1.2.1 stringr_1.4.0
## [27] digest_0.6.25 Rsamtools_2.4.0
## [29] rmarkdown_2.4 XVector_0.28.0
## [31] pkgconfig_2.0.3 htmltools_0.5.0
## [33] dbplyr_1.4.4 limma_3.44.3
## [35] rlang_0.4.8 rstudioapi_0.11
## [37] RSQLite_2.2.1 generics_0.0.2
## [39] jsonlite_1.7.1 BiocParallel_1.22.0
## [41] RCurl_1.98-1.2 magrittr_1.5
## [43] GenomeInfoDbData_1.2.3 futile.logger_1.4.3
## [45] Matrix_1.2-18 Rcpp_1.0.5
## [47] fansi_0.4.1 lifecycle_0.2.0
## [49] stringi_1.5.3 yaml_2.2.1
## [51] RaggedExperiment_1.12.0 RJSONIO_1.3-1.4
## [53] zlibbioc_1.34.0 BiocFileCache_1.12.1
## [55] grid_4.0.3 blob_1.2.1
## [57] crayon_1.3.4 lattice_0.20-41
## [59] Biostrings_2.56.0 splines_4.0.3
## [61] GenomicFeatures_1.40.1 hms_0.5.3
## [63] ps_1.4.0 knitr_1.30
## [65] pillar_1.4.6 codetools_0.2-16
## [67] biomaRt_2.44.4 futile.options_1.0.1
## [69] XML_3.99-0.5 glue_1.4.2
## [71] evaluate_0.14 lambda.r_1.2.4
## [73] data.table_1.13.0 BiocManager_1.30.10
## [75] vctrs_0.3.4 tidyr_1.1.2
## [77] openssl_1.4.3 purrr_0.3.4
## [79] assertthat_0.2.1 xfun_0.18
## [81] survival_3.2-7 tibble_3.0.4
## [83] RTCGAToolbox_2.18.0 GenomicAlignments_1.24.0
## [85] AnnotationDbi_1.50.3 memoise_1.1.0
## [87] ellipsis_0.3.1