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View Code? Open in Web Editor NEWThis is a version of topGO using roxygen2 and Rmd
This is a version of topGO using roxygen2 and Rmd
runTest{topGOdata, character, character}
it uses .algoClass to search for parentchild, but then it is converted to "pC"
From support:
goID <- "GO:0005730"
gt <- printGenes(GOdata, whichTerms = goID,
chip = "org.At.tair.db", numChar = 40)
Error in data.frame(LL.id = as.integer(unlist(mget(all.genes, envir = LL.lib, :
arguments imply differing number of rows: 255, 444
According to that node I have 243 of 255 genes annotated
I have encountered the following issue:
library(topGO)
library(org.Sc.sgd.db)
allGO2genes <- annFUN.org(whichOnto = "BP", feasibleGenes = NULL, mapping = "org.Sc.sgd.db", ID = "genename")
Error: no such table: gene_info
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] org.Sc.sgd.db_3.19.1 topGO_2.55.0 SparseM_1.81 GO.db_3.19.1 AnnotationDbi_1.65.2 IRanges_2.37.1
[7] S4Vectors_0.41.7 Biobase_2.63.1 graph_1.81.1 BiocGenerics_0.49.1
loaded via a namespace (and not attached):
[1] bit_4.0.5 jsonlite_1.8.8 compiler_4.4.0 BiocManager_1.30.22 renv_1.0.7
[6] crayon_1.5.2 blob_1.2.4 Biostrings_2.71.6 png_0.1-8 fastmap_1.1.1
[11] lattice_0.22-6 R6_2.5.1 XVector_0.43.1 GenomeInfoDb_1.39.14 knitr_1.46
[16] GenomeInfoDbData_1.2.12 DBI_1.2.2 rlang_1.1.3 KEGGREST_1.43.0 cachem_1.0.8
[21] xfun_0.43 bit64_4.0.5 RSQLite_2.3.6 memoise_2.0.1 cli_3.6.2
[26] zlibbioc_1.49.3 grid_4.4.0 rstudioapi_0.16.0 vctrs_0.6.5 httr_1.4.7
[31] matrixStats_1.3.0 tools_4.4.0 pkgconfig_2.0.3 UCSC.utils_0.99.7
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