vjcitn
commented
5 years ago we should try to rewrite using curatedTCGAData package who is handling video revisions?
On Mon, Aug 26, 2019 at 7:53 AM gillsignals notifications@github.com wrote:
The TCGA firehose data download on tcga.Rmd line 49 https://github.com/genomicsclass/labs/blob/9ac47c7099a8a2452813c4bb675c21010f5becec/biocadv_6x/tcga.Rmd#L49 throws an error stating the connection cannot be opened:
library(ph525x) firehose() library(RTCGAToolbox) readData = getFirehoseData (dataset="READ", runDate="20150402",forceDownload = TRUE,
- Clinic=TRUE, Mutation=TRUE, Methylation=TRUE, RNASeq2GeneNorm=TRUE) gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz' Content type 'application/x-gzip' length 4754 bytes downloaded 4754 bytes
gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0 gdac.broadinstitute.org_READ.Merge_rnaseqv2illuminaga_rnaseqv2__unc_eduLevel_3RSEM_genes_normalizeddata.Level_3.2015040200.0.0.tar.gzgdac.broadinstitute.org_READ.Merge_rnaseqv2illuminahiseq_rnaseqv2__unc_eduLevel_3RSEM_genes_normalizeddata.Level_3.2015040200.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz' Content type 'application/x-gzip' length 5917492 bytes (5.6 MB) downloaded 5.6 MB
gdac.broadinstitute.org_READ.Merge_rnaseqv2illuminaga_rnaseqv2__unc_eduLevel_3RSEM_genes_normalizeddata.Level_3.2015040200.0.0 cannot open file './20150402-READ-RNAseq2GeneNorm.txt': No such file or directoryError in file(file, "rt") : cannot open the connection
Much of the following code in the section and the related course videos depend on the output of this command.
In addition, the following code block on line 53 appears to read a local path on your machine.
Here is the sessionInfo:
sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages: [1] grid tools parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] RTCGAToolbox_2.14.0 ph525x_0.0.48 png_0.1-7 [4] yeastCC_1.24.0 harbChIP_1.22.0 Biostrings_2.52.0 [7] XVector_0.24.0 ERBS_1.0 gwascat_2.16.0 [10] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.8.2 [13] GO.db_3.8.2 OrganismDbi_1.26.0 GenomicFeatures_1.36.4 [16] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 ggbio_1.32.0 [19] ggplot2_3.2.1 AnnotationDbi_1.46.1 IRanges_2.18.1 [22] S4Vectors_0.22.0 Biobase_2.44.0 BiocGenerics_0.30.0
loaded via a namespace (and not attached): [1] ProtGenerics_1.16.0 bitops_1.0-6 matrixStats_0.54.0 bit64_0.9-7 [5] RColorBrewer_1.1-2 progress_1.2.2 httr_1.4.1 backports_1.1.4 [9] R6_2.4.0 rpart_4.1-15 Hmisc_4.2-0 DBI_1.0.0 [13] lazyeval_0.2.2 colorspace_1.4-1 nnet_7.3-12 withr_2.1.2 [17] tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 GGally_1.4.0 [21] bit_1.1-14 curl_4.0 compiler_3.6.1 graph_1.62.0 [25] htmlTable_1.13.1 DelayedArray_0.10.0 rtracklayer_1.44.2 scales_1.0.0 [29] checkmate_1.9.4 RBGL_1.60.0 RCircos_1.2.1 stringr_1.4.0 [33] digest_0.6.20 Rsamtools_2.0.0 foreign_0.8-71 base64enc_0.1-3 [37] dichromat_2.0-0 pkgconfig_2.0.2 htmltools_0.3.6 limma_3.40.6 [41] ensembldb_2.8.0 BSgenome_1.52.0 htmlwidgets_1.3 rlang_0.4.0 [45] rstudioapi_0.10 RSQLite_2.1.2 BiocParallel_1.18.1 acepack_1.4.1 [49] dplyr_0.8.3 VariantAnnotation_1.30.1 RCurl_1.95-4.12 magrittr_1.5 [53] GenomeInfoDbData_1.2.1 Formula_1.2-3 Matrix_1.2-17 Rcpp_1.0.1 [57] munsell_0.5.0 stringi_1.4.3 RaggedExperiment_1.8.0 RJSONIO_1.3-1.2 [61] SummarizedExperiment_1.14.1 zlibbioc_1.30.0 plyr_1.8.4 blob_1.2.0 [65] crayon_1.3.4 lattice_0.20-38 splines_3.6.1 hms_0.5.1 [69] zeallot_0.1.0 knitr_1.24 pillar_1.4.2 reshape2_1.4.3 [73] biomaRt_2.40.4 XML_3.98-1.20 glue_1.3.1 biovizBase_1.32.0 [77] latticeExtra_0.6-28 BiocManager_1.30.4 data.table_1.12.2 vctrs_0.2.0 [81] gtable_0.3.0 purrr_0.3.2 reshape_0.8.8 assertthat_0.2.1 [85] xfun_0.9 AnnotationFilter_1.8.0 survival_2.44-1.1 tibble_2.1.3 [89] GenomicAlignments_1.20.1 memoise_1.1.0 cluster_2.1.0
Thanks!
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The TCGA firehose data download on tcga.Rmd line 49 throws an error stating the connection cannot be opened:
Much of the following code in the section and the related course videos depend on the output of this command.
In addition, the following code block on line 53 appears to read a local path on your machine.
Here is the
sessionInfo:Thanks!