Hi all,
I'm using PANTHER.db to run some enrichment analysis and am trying to use the function pthOrganisms to restrict the database to mouse. More specifically, the code is:
pthOrganisms(PANTHER.db) = "MOUSE"
However, I obtained the following error:
Error: could not find function "pthOrganisms"
The package installs just fine and the library loads correctly. Page 3 of the vignette (https://bioconductor.org/packages/release/data/annotation/vignettes/PANTHER.db/inst/doc/PANTHER.db.pdf) shows how to use the command, and my code matches exactly. I also tried PANTHER.db::pthOrganisms(PANTHER.db) = "MOUSE" but still obtained the same error. Any tips on how to proceed?
Thanks very much!
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Mm.eg.db_3.0.0 biomaRt_2.22.0 TxDb.Mmusculus.UCSC.mm10.ensGene_3.0.0
[4] GenomicFeatures_1.18.7 reactome.db_1.48.0 PANTHER.db_1.0.1
[7] KEGGREST_1.6.4 goseq_1.18.0 AnnotationDbi_1.28.2
[10] Biobase_2.26.0 RSQLite_1.0.0 DBI_0.3.1
[13] geneLenDataBase_1.1.1 BiasedUrn_1.06.1 XVector_0.6.0
[16] BiocInstaller_1.16.5 pheatmap_1.0.2 ggplot2_1.0.1
[19] data.table_1.9.4 dplyr_0.4.1 plyr_1.8.2
[22] tidyr_0.2.0 Rsubread_1.16.1 DESeq2_1.6.3
[25] RcppArmadillo_0.5.100.1.0 Rcpp_0.11.6 rtracklayer_1.26.3
[28] GenomicRanges_1.18.4 GenomeInfoDb_1.2.5 IRanges_2.0.1
[31] S4Vectors_0.4.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 annotate_1.44.0 assertthat_0.1 base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9
[7] BiocParallel_1.0.3 Biostrings_2.34.1 bitops_1.0-6 brew_1.0-6 checkmate_1.5.3 chron_2.3-45
[13] cluster_2.0.1 codetools_0.2-11 colorspace_1.2-6 digest_0.6.8 fail_1.2 foreach_1.4.2
[19] foreign_0.8-63 Formula_1.2-1 genefilter_1.48.1 geneplotter_1.44.0 GenomicAlignments_1.2.2 GO.db_3.0.0
[25] grid_3.1.2 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.16-0 httr_0.6.1 iterators_1.0.7
[31] labeling_0.3 lattice_0.20-31 latticeExtra_0.6-26 locfit_1.5-9.1 magrittr_1.5 MASS_7.3-40
[37] Matrix_1.2-0 mgcv_1.8-6 munsell_0.4.2 nlme_3.1-120 nnet_7.3-9 png_0.1-7
[43] proto_0.3-10 RColorBrewer_1.1-2 RCurl_1.95-4.6 reshape2_1.4.1 rpart_4.1-9 Rsamtools_1.18.3
[49] scales_0.2.4 sendmailR_1.2-1 splines_3.1.2 stringi_0.4-1 stringr_1.0.0 survival_2.38-1
[55] tools_3.1.2 XML_3.98-1.1 xtable_1.7-4 zlibbioc_1.12.0