Query
library(TCGAbiolinks)
library(SummarizedExperiment)
query <- GDCquery(
project = "NCICCR-DLBCL",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts"
)dim(query$results[[1]])## [1] 481 29Download
GDCdownload(query, method = "api", files.per.chunk = 40)Prepare
counts <- GDCprepare(query = query)Data
counts## class: RangedSummarizedExperiment
## dim: 60660 481
## metadata(1): data_release
## assays(6): unstranded stranded_first ... fpkm_unstrand fpkm_uq_unstrand
## rownames(60660): ENSG00000000003.15 ENSG00000000005.6 ...
## ENSG00000288674.1 ENSG00000288675.1
## rowData names(10): source type ... hgnc_id havana_gene
## colnames(481): DLBCL10490-sample DLBCL10943-sample ...
## DLBCL10842-sample DLBCL11188-sample
## colData names(31): sample sample_submitter_id ... releasable releasedhttps://portal.gdc.cancer.gov/cases/f21fbe58-7b06-43d6-ba44-df03c8b0a748
metadata <- data.frame(colData(counts))
print(
metadata[metadata$sample_submitter_id == "DLBCL10782-sample", c("days_to_last_follow_up","gender","age_at_diagnosis")]
)## days_to_last_follow_up gender age_at_diagnosis
## DLBCL10782-sample 1301 female 25550https://portal.gdc.cancer.gov/cases/1723ef31-df5f-4185-aea8-bcf12077e42e
print(
metadata[metadata$sample_submitter_id == "DLBCL10508-sample", c("days_to_last_follow_up","gender","age_at_diagnosis")]
)## days_to_last_follow_up gender age_at_diagnosis
## DLBCL10508-sample 1147 male 23360sessionInfo
sessionInfo()## R version 4.2.0 (2022-04-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur/Monterey 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] SummarizedExperiment_1.26.1 Biobase_2.56.0
## [3] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
## [5] IRanges_2.30.0 S4Vectors_0.34.0
## [7] BiocGenerics_0.42.0 MatrixGenerics_1.8.0
## [9] matrixStats_0.62.0 TCGAbiolinks_2.25.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 bit64_4.0.5
## [3] filelock_1.0.2 progress_1.2.2
## [5] httr_1.4.3 tools_4.2.0
## [7] bslib_0.3.1 utf8_1.2.2
## [9] R6_2.5.1 DBI_1.1.2
## [11] colorspace_2.0-3 tidyselect_1.1.2
## [13] prettyunits_1.1.1 bit_4.0.4
## [15] curl_4.3.2 compiler_4.2.0
## [17] cli_3.3.0 rvest_1.0.2
## [19] xml2_1.3.3 DelayedArray_0.22.0
## [21] sass_0.4.1 scales_1.2.0
## [23] readr_2.1.2 rappdirs_0.3.3
## [25] stringr_1.4.0 digest_0.6.29
## [27] rmarkdown_2.14 XVector_0.36.0
## [29] pkgconfig_2.0.3 htmltools_0.5.2
## [31] dbplyr_2.2.0 fastmap_1.1.0
## [33] rlang_1.0.2 rstudioapi_0.13
## [35] RSQLite_2.2.14 prettydoc_0.4.1
## [37] jquerylib_0.1.4 generics_0.1.2
## [39] jsonlite_1.8.0 dplyr_1.0.9
## [41] RCurl_1.98-1.7 magrittr_2.0.3
## [43] GenomeInfoDbData_1.2.8 Matrix_1.4-1
## [45] Rcpp_1.0.8.3 munsell_0.5.0
## [47] fansi_1.0.3 lifecycle_1.0.1
## [49] stringi_1.7.6 yaml_2.3.5
## [51] zlibbioc_1.42.0 plyr_1.8.7
## [53] BiocFileCache_2.4.0 grid_4.2.0
## [55] blob_1.2.3 crayon_1.5.1
## [57] lattice_0.20-45 Biostrings_2.64.0
## [59] hms_1.1.1 KEGGREST_1.36.2
## [61] knitr_1.39 pillar_1.7.0
## [63] TCGAbiolinksGUI.data_1.16.0 biomaRt_2.52.0
## [65] XML_3.99-0.10 glue_1.6.2
## [67] evaluate_0.15 downloader_0.4
## [69] data.table_1.14.2 png_0.1-7
## [71] vctrs_0.4.1 tzdb_0.3.0
## [73] gtable_0.3.0 purrr_0.3.4
## [75] tidyr_1.2.0 assertthat_0.2.1
## [77] cachem_1.0.6 ggplot2_3.3.6
## [79] xfun_0.31 tibble_3.1.7
## [81] AnnotationDbi_1.58.0 memoise_2.0.1
## [83] ellipsis_0.3.2