library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-BRCA",
data.category = "Clinical",
data.type = "Clinical Supplement",
data.format = "BCR Biotab")
GDCdownload(query)
clinical.BCRtab.all <- GDCprepare(query)## [1] "clinical_follow_up_v4.0_brca" "clinical_follow_up_v2.1_brca"
## [3] "clinical_drug_brca" "clinical_follow_up_v4.0_nte_brca"
## [5] "clinical_follow_up_v1.5_brca" "clinical_omf_v4.0_brca"
## [7] "clinical_radiation_brca" "clinical_nte_brca"
## [9] "clinical_patient_brca"# colnames from clinical_patient_brca
tibble::tibble(sort(colnames(clinical.BCRtab.all$clinical_patient_brca)))# Biospecimen BCR Biotab
query.biospecimen <- GDCquery(project = "TCGA-BRCA",
data.category = "Biospecimen",
data.type = "Biospecimen Supplement",
data.format = "BCR Biotab")
GDCdownload(query.biospecimen)
biospecimen.BCRtab.all <- GDCprepare(query.biospecimen)## [1] "ssf_tumor_samples_brca"
## [2] "biospecimen_analyte_brca"
## [3] "biospecimen_portion_brca"
## [4] "biospecimen_slide_brca"
## [5] "biospecimen_diagnostic_slides_brca"
## [6] "ssf_normal_controls_brca"
## [7] "biospecimen_shipment_portion_brca"
## [8] "biospecimen_sample_brca"
## [9] "biospecimen_protocol_brca"
## [10] "biospecimen_aliquot_brca"## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 19.04
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
##
## 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=en_US.UTF-8
## [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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] TCGAbiolinks_2.13.6
##
## loaded via a namespace (and not attached):
## [1] backports_1.1.5 circlize_0.4.8
## [3] aroma.light_3.14.0 plyr_1.8.4
## [5] selectr_0.4-1 ConsensusClusterPlus_1.48.0
## [7] lazyeval_0.2.2 splines_3.6.1
## [9] BiocParallel_1.18.1 crosstalk_1.0.0
## [11] GenomeInfoDb_1.20.0 ggplot2_3.2.1
## [13] sva_3.32.1 digest_0.6.22
## [15] foreach_1.4.7 htmltools_0.4.0
## [17] magrittr_1.5 memoise_1.1.0
## [19] cluster_2.1.0 doParallel_1.0.15
## [21] limma_3.40.6 ComplexHeatmap_2.1.2
## [23] Biostrings_2.52.0 readr_1.3.1
## [25] annotate_1.62.0 matrixStats_0.55.0
## [27] R.utils_2.9.0 prettyunits_1.0.2
## [29] colorspace_1.4-1 blob_1.2.0
## [31] rvest_0.3.4 ggrepel_0.8.1
## [33] xfun_0.10 dplyr_0.8.3
## [35] crayon_1.3.4 RCurl_1.95-4.12
## [37] jsonlite_1.6 genefilter_1.66.0
## [39] zeallot_0.1.0 survival_2.44-1.1
## [41] zoo_1.8-6 iterators_1.0.12
## [43] glue_1.3.1 survminer_0.4.6
## [45] gtable_0.3.0.9000 zlibbioc_1.30.0
## [47] XVector_0.24.0 GetoptLong_0.1.7
## [49] DelayedArray_0.10.0 shape_1.4.4
## [51] BiocGenerics_0.30.0 scales_1.0.0
## [53] DESeq_1.36.0 DBI_1.0.0
## [55] edgeR_3.26.8 ggthemes_4.2.0
## [57] Rcpp_1.0.2 xtable_1.8-4
## [59] progress_1.2.2 clue_0.3-57
## [61] bit_1.1-14 matlab_1.0.2
## [63] km.ci_0.5-2 stats4_3.6.1
## [65] DT_0.9 htmlwidgets_1.5.1
## [67] httr_1.4.1 RColorBrewer_1.1-2
## [69] pkgconfig_2.0.3 XML_3.98-1.20
## [71] R.methodsS3_1.7.1 locfit_1.5-9.1
## [73] tidyselect_0.2.5 rlang_0.4.0
## [75] later_1.0.0 AnnotationDbi_1.46.1
## [77] munsell_0.5.0 tools_3.6.1
## [79] downloader_0.4 generics_0.0.2
## [81] RSQLite_2.1.2 broom_0.5.2
## [83] evaluate_0.14 stringr_1.4.0
## [85] fastmap_1.0.1 yaml_2.2.0
## [87] knitr_1.25 bit64_0.9-7
## [89] survMisc_0.5.5 purrr_0.3.3
## [91] EDASeq_2.18.0 nlme_3.1-141
## [93] mime_0.7 R.oo_1.22.0
## [95] xml2_1.2.2 biomaRt_2.40.5
## [97] compiler_3.6.1 curl_4.2
## [99] png_0.1-7 ggsignif_0.6.0
## [101] tibble_2.1.3 geneplotter_1.62.0
## [103] stringi_1.4.3 GenomicFeatures_1.36.4
## [105] lattice_0.20-38 Matrix_1.2-17
## [107] KMsurv_0.1-5 vctrs_0.2.0
## [109] pillar_1.4.2 lifecycle_0.1.0
## [111] GlobalOptions_0.1.1 data.table_1.12.6
## [113] bitops_1.0-6 httpuv_1.5.2
## [115] rtracklayer_1.44.4 GenomicRanges_1.36.1
## [117] R6_2.4.0 latticeExtra_0.6-28
## [119] hwriter_1.3.2 promises_1.1.0
## [121] ShortRead_1.42.0 gridExtra_2.3
## [123] IRanges_2.18.3 codetools_0.2-16
## [125] assertthat_0.2.1 SummarizedExperiment_1.14.1
## [127] rjson_0.2.20 GenomicAlignments_1.20.1
## [129] Rsamtools_2.0.3 S4Vectors_0.22.1
## [131] GenomeInfoDbData_1.2.1 mgcv_1.8-29
## [133] parallel_3.6.1 hms_0.5.1
## [135] grid_3.6.1 tidyr_1.0.0
## [137] rmarkdown_1.16 ggpubr_0.2.3
## [139] Biobase_2.44.0 shiny_1.4.0
## [141] base64enc_0.1-3