Libs
library(TCGAWorkflowData)
library(DT)
library(DESeq2)
library(TCGAbiolinks)
library(TCGAbiolinksGUI.data)
GBM
query.met.gbm <- GDCquery(
project = "TCGA-GBM",
legacy = FALSE,
data.category = "DNA Methylation",
platform = "Illumina Human Methylation 450",
data.type = "Methylation Beta Value",
barcode = c("TCGA-76-4926-01B-01D-1481-05", "TCGA-28-5211-01C-11D-1844-05")
)
GDCdownload(query.met.gbm)
met.gbm.450 <- GDCprepare(
query = query.met.gbm,
save = FALSE,
save.filename = "gbmDNAmet450k.rda",
summarizedExperiment = TRUE
)
## class: RangedSummarizedExperiment
## dim: 485577 2
## metadata(1): data_release
## assays(1): ''
## rownames(485577): cg13869341 cg14008030 ... cg11478607 cg08417382
## rowData names(52): address_A address_B ... MASK_extBase MASK_general
## colnames(2): TCGA-76-4926-01B-01D-1481-05 TCGA-28-5211-01C-11D-1844-05
## colData names(1): samples
LGG
query.met.lgg <- GDCquery(
project = "TCGA-LGG",
legacy = FALSE,
data.category = "DNA Methylation",
data.type = "Methylation Beta Value",
platform = "Illumina Human Methylation 450",
barcode = c("TCGA-HT-7879-01A-11D-2399-05", "TCGA-HT-8113-01A-11D-2399-05")
)
GDCdownload(query.met.lgg)
met.lgg.450 <- GDCprepare(
query = query.met.lgg,
save = FALSE,
save.filename = "lggDNAmet450k.rda",
summarizedExperiment = TRUE
)
## class: RangedSummarizedExperiment
## dim: 485577 2
## metadata(1): data_release
## assays(1): ''
## rownames(485577): cg13869341 cg14008030 ... cg11478607 cg08417382
## rowData names(52): address_A address_B ... MASK_extBase MASK_general
## colnames(2): TCGA-HT-7879-01A-11D-2399-05 TCGA-HT-8113-01A-11D-2399-05
## colData names(1): samples
Merging
met.gbm.lgg <- SummarizedExperiment::cbind(met.lgg.450, met.gbm.450)
met.gbm.lgg
## class: RangedSummarizedExperiment
## dim: 485577 4
## metadata(2): data_release data_release
## assays(1): ''
## rownames(485577): cg13869341 cg14008030 ... cg11478607 cg08417382
## rowData names(52): address_A address_B ... MASK_extBase MASK_general
## colnames(4): TCGA-HT-7879-01A-11D-2399-05 TCGA-HT-8113-01A-11D-2399-05
## TCGA-76-4926-01B-01D-1481-05 TCGA-28-5211-01C-11D-1844-05
## colData names(1): samples
sessionInfo
## R version 4.2.0 alpha (2022-04-06 r82104)
## 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] sesameData_1.13.36 ExperimentHub_2.3.7
## [3] AnnotationHub_3.3.11 BiocFileCache_2.3.4
## [5] dbplyr_2.1.1 TCGAbiolinksGUI.data_1.15.1
## [7] TCGAbiolinks_2.23.11 DESeq2_1.35.0
## [9] SummarizedExperiment_1.25.3 Biobase_2.55.2
## [11] MatrixGenerics_1.7.0 matrixStats_0.61.0
## [13] GenomicRanges_1.47.6 GenomeInfoDb_1.31.7
## [15] IRanges_2.29.1 S4Vectors_0.33.17
## [17] BiocGenerics_0.41.2 DT_0.22
## [19] TCGAWorkflowData_1.19.1
##
## loaded via a namespace (and not attached):
## [1] wheatmap_0.2.0 colorspace_2.0-3
## [3] ellipsis_0.3.2 XVector_0.35.0
## [5] rstudioapi_0.13 bit64_4.0.5
## [7] interactiveDisplayBase_1.33.0 AnnotationDbi_1.57.1
## [9] fansi_1.0.3 xml2_1.3.3
## [11] splines_4.2.0 R.methodsS3_1.8.1
## [13] cachem_1.0.6 geneplotter_1.73.0
## [15] knitr_1.38 jsonlite_1.8.0
## [17] annotate_1.73.0 png_0.1-7
## [19] R.oo_1.24.0 shiny_1.7.1
## [21] BiocManager_1.30.16 readr_2.1.2
## [23] compiler_4.2.0 httr_1.4.2
## [25] assertthat_0.2.1 Matrix_1.4-1
## [27] fastmap_1.1.0 cli_3.2.0
## [29] later_1.3.0 htmltools_0.5.2
## [31] prettyunits_1.1.1 tools_4.2.0
## [33] gtable_0.3.0 glue_1.6.2
## [35] GenomeInfoDbData_1.2.8 reshape2_1.4.4
## [37] dplyr_1.0.8 rappdirs_0.3.3
## [39] Rcpp_1.0.8.3 jquerylib_0.1.4
## [41] vctrs_0.4.1 Biostrings_2.63.3
## [43] preprocessCore_1.57.1 xfun_0.30
## [45] stringr_1.4.0 rvest_1.0.2
## [47] mime_0.12 lifecycle_1.0.1
## [49] XML_3.99-0.9 zlibbioc_1.41.0
## [51] scales_1.2.0 promises_1.2.0.1
## [53] hms_1.1.1 parallel_4.2.0
## [55] RColorBrewer_1.1-3 yaml_2.3.5
## [57] curl_4.3.2 memoise_2.0.1
## [59] ggplot2_3.3.5 downloader_0.4
## [61] sass_0.4.1 biomaRt_2.51.4
## [63] stringi_1.7.6 RSQLite_2.2.12
## [65] BiocVersion_3.15.2 genefilter_1.77.1
## [67] filelock_1.0.2 BiocParallel_1.29.20
## [69] rlang_1.0.2 pkgconfig_2.0.3
## [71] bitops_1.0-7 sesame_1.13.47
## [73] evaluate_0.15 lattice_0.20-45
## [75] purrr_0.3.4 htmlwidgets_1.5.4
## [77] bit_4.0.4 tidyselect_1.1.2
## [79] plyr_1.8.7 magrittr_2.0.3
## [81] R6_2.5.1 generics_0.1.2
## [83] DelayedArray_0.21.2 DBI_1.1.2
## [85] withr_2.5.0 pillar_1.7.0
## [87] survival_3.3-1 KEGGREST_1.35.0
## [89] RCurl_1.98-1.6 tibble_3.1.6
## [91] crayon_1.5.1 utf8_1.2.2
## [93] tzdb_0.3.0 rmarkdown_2.13
## [95] progress_1.2.2 locfit_1.5-9.5
## [97] grid_4.2.0 data.table_1.14.2
## [99] blob_1.2.3 digest_0.6.29
## [101] xtable_1.8-4 httpuv_1.6.5
## [103] tidyr_1.2.0 R.utils_2.11.0
## [105] munsell_0.5.0 bslib_0.3.1