I am currently trying to work with goslim on a set of differentially expressed genes of which I have some ontologies.
I tried to use commands similar to those on this link https://www.rdocumentation.org/packages/GSEABase/versions/1.34.0/topics/goSlim-methods
fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase") slim <- getOBOCollection(fl) setDEGOs=as.character(DEGOs$V3) #head(setDEGOs) # "GO:0006354" "GO:0003677" "GO:0016570" "GO:0005515" "GO:0003702" "GO:0005815" currentCollecSet=GOCollection(setDEGOs)
However, I obtain the following error when running GOCollection:
Error: getAnnMap: package GO not available
When I try to install the missing package, this is what I obtain:
>biocLite("GO") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing package(s) ‘GO’ installation path not writeable, unable to update packages: boot, Matrix, mgcv Warning message: package ‘GO’ is not available (for R version 3.4.1)
It seems my R installation is up to date. Any idea what is going on? Is there any other library I should use here?
This is the result of my sessionInfo() command:
R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C  LC_TIME=Danish_Denmark.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  GSEABase_1.38.1 graph_1.54.0 annotate_1.54.0 XML_3.98-1.9 AnnotationDbi_1.38.2 IRanges_2.10.3 S4Vectors_0.14.4  Biobase_2.36.2 BiocGenerics_0.22.0 BiocInstaller_1.26.1 loaded via a namespace (and not attached):  Rcpp_0.12.12 digest_0.6.12 bitops_1.0-6 xtable_1.8-2 DBI_0.7 RSQLite_2.0 rlang_0.1.2 blob_1.1.0 tools_3.4.1 bit64_0.9-7  RCurl_1.95-4.8 bit_1.1-12 compiler_3.4.1 memoise_1.1.0 tibble_1.3.4
Best regards and thanks for reading!