Entering edit mode
Hi there,
I am trying to download the "bt.exon_quantification" files using TCGAbiolinks but I'm running into a bug:
library(TCGAbiolinks) prad <- TCGAquery(tumor = "prad", platform = "IlluminaHiSeq_RNASeqV2", level = 3) TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification")
returns the error message:
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
| Downloading:550 files
| Path:~/Documents/rawdata//unc.edu_PRAD.IlluminaHiSeq_RNASeqV2.Level_3.1.14.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
| | 0%
Error in if (force || !file.exists(file.path(path, folder, files[i])) || :
missing value where TRUE/FALSE needed
traceback() 1: TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification")
sessionInfo() R Under development (unstable) (2015-11-25 r69695) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.04 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TCGAbiolinks_1.1.26 loaded via a namespace (and not attached): [1] circlize_0.3.5 aroma.light_3.1.1 plyr_1.8.3 [4] igraph_1.0.1 ConsensusClusterPlus_1.35.0 splines_3.3.0 [7] BiocParallel_1.5.21 GenomeInfoDb_1.7.6 ggplot2_2.1.0 [10] TH.data_1.0-7 digest_0.6.9 foreach_1.4.3 [13] BiocInstaller_1.21.4 rsconnect_0.4.2.1 gdata_2.17.0 [16] magrittr_1.5 memoise_1.0.0 cluster_2.0.3 [19] doParallel_1.0.10 limma_3.27.15 ComplexHeatmap_1.9.5 [22] Biostrings_2.39.12 annotate_1.49.1 matrixStats_0.50.1 [25] R.utils_2.3.0 sandwich_2.3-4 colorspace_1.2-6 [28] rvest_0.3.1 ggrepel_0.5 haven_0.2.0 [31] dplyr_0.4.3 RCurl_1.95-4.8 hexbin_1.27.1 [34] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.49.1 genefilter_1.53.3 [37] lme4_1.1-11 supraHex_1.9.0 survival_2.38-3 [40] zoo_1.7-12 iterators_1.0.8 ape_3.4 [43] gtable_0.2.0 zlibbioc_1.17.1 XVector_0.11.8 [46] MatrixModels_0.4-1 GetoptLong_0.1.2 sjmisc_1.7 [49] car_2.1-2 Rgraphviz_2.15.0 shape_1.4.2 [52] BiocGenerics_0.17.5 SparseM_1.7 scales_0.4.0 [55] DESeq_1.23.1 mvtnorm_1.0-5 DBI_0.3.1 [58] GGally_1.0.1 edgeR_3.13.8 Rcpp_0.12.4 [61] xtable_1.8-2 matlab_1.0.2 preprocessCore_1.33.0 [64] stats4_3.3.0 httr_1.1.0 gplots_3.0.1 [67] RColorBrewer_1.1-2 modeltools_0.2-21 reshape_0.8.5 [70] XML_3.98-1.4 R.methodsS3_1.7.1 nnet_7.3-12 [73] reshape2_1.4.1 AnnotationDbi_1.33.8 munsell_0.4.3 [76] tools_3.3.0 downloader_0.4 RSQLite_1.0.0 [79] devtools_1.11.0 stringr_1.0.0 knitr_1.12.3 [82] caTools_1.17.1 dendextend_1.1.8 coin_1.1-2 [85] EDASeq_2.5.1 nlme_3.1-126 quantreg_5.21 [88] whisker_0.3-2 R.oo_1.20.0 xml2_0.1.2 [91] biomaRt_2.27.2 pbkrtest_0.4-6 curl_0.9.7 [94] affyio_1.41.0 geneplotter_1.49.0 stringi_1.0-1 [97] GenomicFeatures_1.23.27 lattice_0.20-33 Matrix_1.2-4 [100] psych_1.5.8 nloptr_1.0.4 effects_3.1-1 [103] stringdist_0.9.4.1 GlobalOptions_0.0.9 data.table_1.9.6 [106] cowplot_0.6.1 bitops_1.0-6 dnet_1.0.8 [109] rtracklayer_1.31.10 GenomicRanges_1.23.25 R6_2.1.2 [112] latticeExtra_0.6-28 affy_1.49.0 hwriter_1.3.2 [115] ShortRead_1.29.2 KernSmooth_2.23-15 IRanges_2.5.40 [118] codetools_0.2-14 MASS_7.3-45 gtools_3.5.0 [121] assertthat_0.1 chron_2.3-47 SummarizedExperiment_1.1.24 [124] rjson_0.2.15 withr_1.0.1 mnormt_1.5-4 [127] GenomicAlignments_1.7.20 Rsamtools_1.23.8 multcomp_1.4-4 [130] S4Vectors_0.9.44 mgcv_1.8-12 parallel_3.3.0 [133] grid_3.3.0 sjPlot_1.9.4 tidyr_0.4.1 [136] minqa_1.2.4 Biobase_2.31.3
Your help is appreciated! Thank you!
Regards,
Marcel
Hi Marcel,
I'm running the same code and it is working. Also, could you please see if the folder "~/Documents/rawdata/" was created?
-------------------------------------------------------------------------------------------------------------------
> prad <- TCGAquery(tumor = "prad", platform = "IlluminaHiSeq_RNASeqV2", level = 3)
> TCGAdownload(prad, "/home/tiagochst/rawdata", type = "bt.exon_quantification")
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:550 files
| Path:/home/tiagochst/rawdata/unc.edu_PRAD.IlluminaHiSeq_RNASeqV2.Level_3.1.14.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| | 0%
[1] unc.edu.011453b6-9736-4ea4-8845-bbe4416783d3.1755416.bt.exon_quantification.txt
[2] unc.edu.0120b5b1-d204-429a-aa21-704fd98624ea.1755653.bt.exon_quantification.txt
[3] unc.edu.01234d47-e213-401f-b4fe-f33b15bcec7d.2597947.bt.exon_quantification.txt
|= | 1%
[4] unc.edu.01d4c289-6d85-4119-86f5-bcf3de30d0f7.1753232.bt.exon_quantification.txt
[5] unc.edu.02334a5d-c3a2-4ea6-8e4e-d603a8fbc43c.1760313.bt.exon_quantification.txt
[6] unc.edu.024fc1c9-4502-4293-a555-9bb7e5536f45.2602835.bt.exon_quantification.txt
-------------------------------------------------------------------
What I think it is happening is that TCGA was down for some reason. When you specify the type, it access the TCGA to get the files available, then it filter by type. I believe the files variable received NULL in this case and this messed with the test.
Could you try it again? I'll try to figure a way to verify if TCGA is available or not and alert the user. This is missing in the code.
I hope it works.
Best regards,
Tiago