Question: goseq package: cannot find function supportedOrganisms()
0
gravatar for mrodrigues.fernanda
3.1 years ago by
United States
mrodrigues.fernanda40 wrote:

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; • 1.4k views
ADD COMMENTlink written 3.1 years ago by mrodrigues.fernanda40

I can't find a reference to a function named supportedOrganisms in the goseq package, maybe you mean supportedGenomes?

ADD REPLYlink written 3.1 years ago by James Ashmore2.6k

I found it here: https://bioconductor.org/packages/3.3/bioc/vignettes/goseq/inst/doc/goseq.pdf

Maybe it has been replaced by supportedGenomes() ?

ADD REPLYlink written 3.1 years ago by mrodrigues.fernanda40
1
gravatar for James Ashmore
3.1 years ago by
James Ashmore2.6k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.6k wrote:

It looks to be the case, I had a look in the geneLenDataBase package which you also need and they only have a reference to a function called supportedGenomes. Try that instead.

EDIT:

The developmental version of goseq has the function supportedOrganisms. Install the developmental version.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by James Ashmore2.6k

You're right. I installed the development version and the function is there. Thank you so much, James! You were very helpful.

ADD REPLYlink written 3.1 years ago by mrodrigues.fernanda40
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