downloader::download(
url = "https://api.gdc.cancer.gov/data/7d64377f-2cea-4ee3-917f-8fcfbcd999e7",
"all_thresholded.by_genes_whitelisted.tsv"
)
gistic.pancan <- readr::read_tsv("all_thresholded.by_genes_whitelisted.tsv")brca.gistic.firehose <- TCGAbiolinks::getGistic("BRCA", type = "thresholded")
brca.gistic.pancan <- gistic.pancan[colnames(gistic.pancan) %in% colnames(brca.gistic.firehose)]
brca.gistic.firehose <- brca.gistic.firehose[colnames(brca.gistic.firehose) %in% colnames(gistic.pancan)]
brca.gistic.pancan <- gistic.pancan[match(colnames(brca.gistic.firehose),colnames(gistic.pancan))]## [1] "Gene Symbol" "Locus ID"
## [3] "Cytoband" "TCGA-3C-AAAU-01A-11D-A41E-01"
## [5] "TCGA-3C-AALI-01A-11D-A41E-01" "TCGA-3C-AALJ-01A-31D-A41E-01"## [1] "Gene Symbol" "Locus ID"
## [3] "Cytoband" "TCGA-3C-AAAU-01A-11D-A41E-01"
## [5] "TCGA-3C-AALI-01A-11D-A41E-01" "TCGA-3C-AALJ-01A-31D-A41E-01"## [1] TRUE##
## FALSE TRUE
## 19 1054## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 19.10
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-08-10
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## abind 1.4-5 2016-07-21 [2] CRAN (R 3.6.1)
## annotate 1.64.0 2019-10-29 [2] Bioconductor
## AnnotationDbi 1.48.0 2019-10-29 [2] Bioconductor
## AnnotationHub * 2.18.0 2019-10-29 [2] Bioconductor
## aroma.light 3.16.0 2019-10-29 [2] Bioconductor
## askpass 1.1 2019-01-13 [2] CRAN (R 3.6.1)
## assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
## backports 1.1.8 2020-06-17 [2] CRAN (R 3.6.1)
## Biobase * 2.46.0 2019-10-29 [2] Bioconductor
## BiocFileCache * 1.10.2 2019-11-08 [2] Bioconductor
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## biomaRt 2.42.1 2020-03-26 [2] Bioconductor
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## data.table 1.13.0 2020-07-24 [2] CRAN (R 3.6.1)
## DBI 1.1.0 2019-12-15 [2] CRAN (R 3.6.1)
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## devtools 2.3.1 2020-07-21 [2] CRAN (R 3.6.1)
## digest 0.6.25 2020-02-23 [2] CRAN (R 3.6.1)
## DNAcopy 1.60.0 2019-10-29 [2] Bioconductor
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## downloader 0.4 2015-07-09 [2] CRAN (R 3.6.1)
## dplyr * 1.0.1 2020-07-31 [2] CRAN (R 3.6.1)
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## fs 1.5.0 2020-07-31 [2] CRAN (R 3.6.1)
## genefilter 1.68.0 2019-10-29 [2] Bioconductor
## geneplotter 1.64.0 2019-10-29 [2] Bioconductor
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## GenomeInfoDbData 1.2.2 2019-12-02 [2] Bioconductor
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## GenomicFeatures 1.38.2 2020-02-15 [2] Bioconductor
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## httr 1.4.2 2020-07-20 [2] CRAN (R 3.6.1)
## hwriter 1.3.2 2014-09-10 [2] CRAN (R 3.6.1)
## impute * 1.60.0 2019-10-29 [2] Bioconductor
## interactiveDisplayBase 1.24.0 2019-10-29 [2] Bioconductor
## IRanges * 2.20.2 2020-01-13 [2] Bioconductor
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## jpeg 0.1-8.1 2019-10-24 [2] CRAN (R 3.6.1)
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##
## [1] /home/tiagochst/R/x86_64-pc-linux-gnu-library/3.6
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library