goseq package: cannot find function supportedOrganisms()
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Entering edit mode
@mrodriguesfernanda-9433
Last seen 5.3 years ago
University of Illinois, Urbana-Champaign

Hi! I am trying to use the package goseq, but when I try running the function supportedOrganisms() R says it cannot find it. Does anyone know what might be the reason?

Thanks!

sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base

other attached packages: [1] KEGG.db_3.2.2 goseq_1.22.0
[3] geneLenDataBase_1.6.0 BiasedUrn_1.07
[5] GOstats_2.36.0 graph_1.48.0
[7] Category_2.36.0 GO.db_3.2.2
[9] Matrix_1.2-4 org.Bt.eg.db_3.2.3
[11] AnnotationDbi_1.32.3 edgeR_3.12.0
[13] limma_3.26.9 affycoretools_1.42.0 [15] Biobase_2.30.0 WGCNA_1.51
[17] RSQLite_1.0.0 DBI_0.3.1
[19] fastcluster_1.1.16 dynamicTreeCut_1.63-1 [21] rtracklayer_1.30.4 GenomicRanges_1.22.4 [23] GenomeInfoDb_1.6.3 IRanges_2.4.8
[25] S4Vectors_0.8.11 BiocGenerics_0.16.1

loaded via a namespace (and not attached): [1] nlme_3.1-126 bitops_1.0-6
[3] matrixStats_0.50.1 doParallel_1.0.10
[5] RColorBrewer_1.1-2 gcrma_2.42.0
[7] tools_3.2.4 affyio_1.40.0
[9] KernSmooth_2.23-15 rpart_4.1-10
[11] mgcv_1.8-12 Hmisc_3.17-2
[13] colorspace_1.2-6 nnet_7.3-12
[15] gridExtra_2.2.1 GGally_1.0.1
[17] DESeq2_1.10.1 bit_1.1-12
[19] preprocessCore_1.32.0 ggbio_1.18.5
[21] caTools_1.17.1 scales_0.4.0
[23] genefilter_1.52.1 affy_1.48.0
[25] RBGL_1.46.0 stringr_1.0.0
[27] Rsamtools_1.22.0 foreign_0.8-66
[29] R.utils_2.2.0 AnnotationForge_1.12.2
[31] XVector_0.10.0 dichromat_2.0-0
[33] BSgenome_1.38.0 PFAM.db_3.2.2
[35] impute_1.44.0 BiocInstaller_1.20.1
[37] hwriter_1.3.2 gtools_3.5.0
[39] BiocParallel_1.4.3 acepack_1.3-3.3
[41] R.oo_1.20.0 VariantAnnotation_1.16.4
[43] RCurl_1.95-4.8 magrittr_1.5
[45] Formula_1.2-1 oligoClasses_1.32.0
[47] futile.logger_1.4.1 Rcpp_0.12.4
[49] munsell_0.4.3 R.methodsS3_1.7.1
[51] stringi_1.0-1 SummarizedExperiment_1.0.2 [53] zlibbioc_1.16.0 gplots_3.0.1
[55] plyr_1.8.3 grid_3.2.4
[57] gdata_2.17.0 ReportingTools_2.10.0
[59] lattice_0.20-33 Biostrings_2.38.4
[61] splines_3.2.4 GenomicFeatures_1.22.13
[63] annotate_1.48.0 locfit_1.5-9.1
[65] knitr_1.12.3 geneplotter_1.48.0
[67] reshape2_1.4.1 codetools_0.2-14
[69] biomaRt_2.26.1 futile.options_1.0.0
[71] XML_3.98-1.4 RcppArmadillo_0.6.600.4.0 [73] biovizBase_1.18.0 latticeExtra_0.6-28
[75] lambda.r_1.1.7 foreach_1.4.3
[77] gtable_0.2.0 reshape_0.8.5
[79] ggplot2_2.1.0 xtable_1.8-2
[81] ff_2.2-13 survival_2.38-3
[83] OrganismDbi_1.12.1 iterators_1.0.8
[85] GenomicAlignments_1.6.3 cluster_2.0.3
[87] GSEABase_1.32.0

goseq • 695 views
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Entering edit mode
@nadia-davidson-5739
Last seen 3.3 years ago
Australia

You can use supportedGenomes() and supportedGeneIDs() instead with your version. They give similar information. There's an example in the goseq vignette which matches your version of goseq. The new supportedOrganisms() function is just a bit easier to interpret and proved information about the GO terms support, not just the gene lengths.

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@james-w-macdonald-5106
Last seen 3 days ago
United States

That function is in the devel version, not release.
 

 

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