Entering edit mode
Hi there,
I'm trying to download the Thymoma data from TCGAbiolinks::TCGAquery_maf but I am unable to because I get an error:
thym <- TCGAquery_maf(tumor = "thym")
Error in df$Deploy.Status : $ operator is invalid for atomic vectors
Traceback:
3 subset.default(df, df$Deploy.Status == "Available")
2 subset(df, df$Deploy.Status == "Available")
1 TCGAquery_maf(tumor = "thym")
> 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=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] TCGAbiolinks_1.1.24 loaded via a namespace (and not attached): [1] circlize_0.3.5 aroma.light_3.1.1 selectr_0.2-3 plyr_1.8.3 [5] igraph_1.0.1 ConsensusClusterPlus_1.35.0 splines_3.3.0 BiocParallel_1.5.21 [9] GenomeInfoDb_1.7.6 ggplot2_2.1.0 TH.data_1.0-7 digest_0.6.9 [13] foreach_1.4.3 BiocInstaller_1.21.4 rsconnect_0.4.2.1 gdata_2.17.0 [17] magrittr_1.5 memoise_1.0.0 xlsx_0.5.7 cluster_2.0.3 [21] doParallel_1.0.10 limma_3.27.14 ComplexHeatmap_1.9.4 Biostrings_2.39.12 [25] annotate_1.49.1 matrixStats_0.50.1 R.utils_2.2.0 sandwich_2.3-4 [29] colorspace_1.2-6 rvest_0.3.1 haven_0.2.0 dplyr_0.4.3 [33] RCurl_1.95-4.8 hexbin_1.27.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.49.1 [37] genefilter_1.53.3 lme4_1.1-11 supraHex_1.9.0 survival_2.38-3 [41] zoo_1.7-12 iterators_1.0.8 ape_3.4 gtable_0.2.0 [45] zlibbioc_1.17.1 CNTools_1.27.0 XVector_0.11.7 MatrixModels_0.4-1 [49] GetoptLong_0.1.2 sjmisc_1.6 car_2.1-2 Rgraphviz_2.15.0 [53] shape_1.4.2 BiocGenerics_0.17.3 SparseM_1.7 scales_0.4.0 [57] DESeq_1.23.1 mvtnorm_1.0-5 DBI_0.3.1 GGally_1.0.1 [61] edgeR_3.13.5 Rcpp_0.12.4 xtable_1.8-2 matlab_1.0.2 [65] preprocessCore_1.33.0 stats4_3.3.0 httr_1.1.0 gplots_3.0.1 [69] RColorBrewer_1.1-2 modeltools_0.2-21 rJava_0.9-8 reshape_0.8.5 [73] XML_3.98-1.4 R.methodsS3_1.7.1 nnet_7.3-12 reshape2_1.4.1 [77] AnnotationDbi_1.33.7 munsell_0.4.3 downloader_0.4 RSQLite_1.0.0 [81] devtools_1.10.0 stringr_1.0.0 caTools_1.17.1 dendextend_1.1.8 [85] coin_1.1-2 EDASeq_2.5.1 nlme_3.1-126 whisker_0.3-2 [89] quantreg_5.21 R.oo_1.20.0 xml2_0.1.2 biomaRt_2.27.2 [93] pbkrtest_0.4-6 curl_0.9.6 affyio_1.41.0 geneplotter_1.49.0 [97] stringi_1.0-1 GenomicFeatures_1.23.27 lattice_0.20-33 Matrix_1.2-4 [101] psych_1.5.8 nloptr_1.0.4 effects_3.1-1 stringdist_0.9.4.1 [105] GlobalOptions_0.0.9 data.table_1.9.6 cowplot_0.6.1 bitops_1.0-6 [109] dnet_1.0.7 rtracklayer_1.31.9 GenomicRanges_1.23.25 R6_2.1.2 [113] latticeExtra_0.6-28 affy_1.49.0 hwriter_1.3.2 ShortRead_1.29.2 [117] KernSmooth_2.23-15 IRanges_2.5.40 codetools_0.2-14 MASS_7.3-45 [121] gtools_3.5.0 assertthat_0.1 xlsxjars_0.6.1 chron_2.3-47 [125] SummarizedExperiment_1.1.22 rjson_0.2.15 mnormt_1.5-4 GenomicAlignments_1.7.20 [129] Rsamtools_1.23.6 cghMCR_1.29.0 multcomp_1.4-4 S4Vectors_0.9.44 [133] mgcv_1.8-12 parallel_3.3.0 grid_3.3.0 sjPlot_1.9.4 [137] tidyr_0.4.1 minqa_1.2.4 Biobase_2.31.3 |
|
|
Thank you.
Marcel
Hi Marcel,
thank you for pointing the bug. It will be fixed in version 1.1.25, otherwise you can download from the github repository.
https://github.com/BioinformaticsFMRP/TCGAbiolinks/
Best regards,
Tiago