TCGA-ACC
query <- GDCquery(
project = "TCGA-ACC",
data.category = "Copy Number Variation",
data.type = "Allele-specific Copy Number Segment",
access = "open"
)head(getResults(query)[,"cases"])## [1] "TCGA-OR-A5LO-01A-11D-A29H-01,TCGA-OR-A5LO-10A-01D-A29K-01"
## [2] "TCGA-OR-A5KV-01A-11D-A29H-01,TCGA-OR-A5KV-10A-01D-A29K-01"
## [3] "TCGA-OR-A5JD-01A-11D-A29H-01,TCGA-OR-A5JD-10B-01D-A29K-01"
## [4] "TCGA-OR-A5K6-01A-11D-A29H-01,TCGA-OR-A5K6-10A-01D-A29K-01"
## [5] "TCGA-OR-A5JY-01A-31D-A29H-01,TCGA-OR-A5JY-10A-01D-A29K-01"
## [6] "TCGA-OR-A5LT-01A-11D-A29H-01,TCGA-OR-A5LT-10A-01D-A29K-01"GDCdownload(query)## Downloading data for project TCGA-ACC## Of the 90 files for download 90 already exist.## All samples have been already downloadeddata <- GDCprepare(query)## Reading copy number variation filesdata %>% DT::datatable(filter = 'top', options = list(
pageLength = 5, autoWidth = TRUE
))## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.htmlTCGA-LGG
query <- GDCquery(
project = "TCGA-LGG",
data.category = "Copy Number Variation",
data.type = "Allele-specific Copy Number Segment",
access = "open"
)head(getResults(query)[,"cases"])## [1] "TCGA-TQ-A7RU-01A-21D-A349-01,TCGA-TQ-A7RU-10A-01D-A349-01"
## [2] "TCGA-DU-7010-01A-11D-2023-01,TCGA-DU-7010-10A-01D-2023-01"
## [3] "TCGA-DU-5855-01A-11D-1704-01,TCGA-DU-5855-10A-01D-1704-01"
## [4] "TCGA-S9-A6U1-01A-21D-A33S-01,TCGA-S9-A6U1-10A-01D-A33V-01"
## [5] "TCGA-HT-7481-01A-11D-2023-01,TCGA-HT-7481-10A-01D-2023-01"
## [6] "TCGA-CS-6290-01A-11D-1704-01,TCGA-CS-6290-10A-01D-1704-01"GDCdownload(query)## Downloading data for project TCGA-LGG## Of the 527 files for download 527 already exist.## All samples have been already downloadeddata <- GDCprepare(query)## Reading copy number variation filesdata %>% DT::datatable(filter = 'top', options = list(
pageLength = 5, autoWidth = TRUE
))## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.htmlSession information
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.0 (2022-04-22)
## os macOS Big Sur/Monterey 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/Sao_Paulo
## date 2022-06-23
## pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
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## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
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## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.2.0)
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## processx 3.6.1 2022-06-17 [1] CRAN (R 4.2.0)
## progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0)
## ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
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## VP TCGAbiolinks * 2.25.2 2022-06-16 [?] Bioconductor (on disk 2.24.3)
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## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0)
## XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0)
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## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## V ── Loaded and on-disk version mismatch.
## P ── Loaded and on-disk path mismatch.
##
## ──────────────────────────────────────────────────────────────────────────────