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lucas.michel
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@lucasmichel-20031
Last seen 5.7 years ago
I have created a custom annotation package using makeOrgPackage(). After succesfully creating it, installing it and loading it I have am trying to make a functional enrichment using it's annotations (which is why I created it) using GOstats. I can load it into the params object with no errors but when i call hyperGTest() i get the following error:
*Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘columns’ for signature ‘"function"’*
I am guessing it might have something to do with the name of the custom package (if i call columns("org.PfalciparumPlasmoDB.eg") i get exactly the same error) but I don't know how to fix it.
Thanks
## CODE ##
library("GOstats")
library("GO.db")
library("org.PfalciparumPlasmoDB.eg.db") ## My custom annotation package
## Create universe; only genes with GO BP annotations ##
all_tbl <- AnnotationDbi::select(org.PfalciparumPlasmoDB.eg.db, keys = featureNames(xgene_impute), columns = c("GO"), keytype = "SYMBOL")
ids = keys(org.PfalciparumPlasmoDB.eg.db, "GO")
df = AnnotationDbi::select(GO.db, keys(GO.db), "ONTOLOGY")
bp_ids = ids[ids %in% df$GOID[df$ONTOLOGY == "BP"]]
universeBP <- unique(all_tbl[all_tbl$GO %in% bp_ids, "SYMBOL"])
## Remove genes that have go terms that do not appear in GO.db ##
noGO <- all_tbl[!all_tbl$GO %in% keys(GO.db),]$SYMBOL
universeBP <- universeBP[!universeBP %in% noGO]
## Run FE (hyperGTest) ##
hgCutoff <- 0.05
paramsBP <- new("GOHyperGParams",
geneIds=cl_bp,
universeGeneIds=universeBP,
annotation="org.PfalciparumPlasmoDB.eg.db",
ontology="BP",
pvalueCutoff=hgCutoff,
conditional=FALSE,
testDirection="over")
hgOverBP <- hyperGTest(paramsBP)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘columns’ for signature ‘"function"’
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=es_ES.UTF-8 LC_NAME=es_ES.UTF-8
[9] LC_ADDRESS=es_ES.UTF-8 LC_TELEPHONE=es_ES.UTF-8 LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=es_ES.UTF-8
attached base packages:
[1] stats4 grid parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Pf.plasmo.db_3.7.0 org.PfalciparumPlasmoDB.eg.db_1.0.0 forcats_0.4.0 stringr_1.4.0
[5] purrr_0.3.0 readr_1.3.1 tibble_2.0.1 tidyverse_1.2.1
[9] Rgraphviz_2.26.0 xtable_1.8-3 RColorBrewer_1.1-2 GO.db_3.7.0
[13] GOstats_2.48.0 graph_1.60.0 Category_2.48.0 Matrix_1.2-15
[17] AnnotationForge_1.24.0 AnnotationDbi_1.44.0 IRanges_2.16.0 S4Vectors_0.20.1
[21] kableExtra_1.0.1 ggdendro_0.1-20 venneuler_1.1-0 rJava_0.9-10
[25] pca3d_0.10 gridExtra_2.3 tidyr_0.8.2 dplyr_0.8.0.1
[29] VennDiagram_1.6.20 futile.logger_1.4.3 ggfortify_0.4.5 gplots_3.0.1.1
[33] ggplot2_3.1.0 reshape2_1.4.3 Biobase_2.42.0 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-0 rstudioapi_0.9.0 bit64_0.9-7 lubridate_1.7.4 xml2_1.2.0 splines_3.5.2
[7] knitr_1.21 jsonlite_1.6 broom_0.5.1 annotate_1.60.0 shiny_1.2.0 compiler_3.5.2
[13] httr_1.4.0 backports_1.1.3 assertthat_0.2.0 lazyeval_0.2.1 cli_1.0.1 later_0.8.0
[19] formatR_1.5 htmltools_0.3.6 tools_3.5.2 gtable_0.2.0 glue_1.3.0 Rcpp_1.0.0
[25] cellranger_1.1.0 gdata_2.18.0 nlme_3.1-137 crosstalk_1.0.0 xfun_0.5 rvest_0.3.2
[31] mime_0.6 miniUI_0.1.1.1 gtools_3.8.1 XML_3.98-1.17 MASS_7.3-51.1 scales_1.0.0
[37] hms_0.4.2 promises_1.0.1 RBGL_1.58.1 lambda.r_1.2.3 yaml_2.2.0 memoise_1.1.0
[43] stringi_1.3.1 RSQLite_2.1.1 genefilter_1.64.0 caTools_1.17.1.1 manipulateWidget_0.10.0 rlang_0.3.1
[49] pkgconfig_2.0.2 bitops_1.0-6 rgl_0.99.16 evaluate_0.13 lattice_0.20-38 htmlwidgets_1.3
[55] bit_1.1-14 tidyselect_0.2.5 GSEABase_1.44.0 plyr_1.8.4 magrittr_1.5 R6_2.4.0
[61] generics_0.0.2 DBI_1.0.0 pillar_1.3.1 haven_2.1.0 withr_2.1.2 survival_2.43-3
[67] RCurl_1.95-4.11 modelr_0.1.4 crayon_1.3.4 futile.options_1.0.1 KernSmooth_2.23-15 ellipse_0.4.1
[73] rmarkdown_1.11 readxl_1.3.0 blob_1.1.1 digest_0.6.18 webshot_0.5.1 httpuv_1.4.5.1
[79] munsell_0.5.0 viridisLite_0.3.0
The input IDs for this function should be the central ID for your OrgDb package. Usually that's the Gene ID, but it's not the GO ID because the functions in GOstats will already be trying to map the ID to GO IDs, which obviously won't work. In general the Universe should be the set of genes that you measured (which is probably the set of genes on your microarray), again, using the central ID of your annotation package, which you can get by doing
head(keys(org.PfalciparumPlasmoDB.eg.db)), and which are usually the NCBI Gene ID, but may be different for you.The error is mysterious to me. The only place in either GOstats or Category that calls
columnson anything is in a function for Yeast arrays. Which should only happen if you get YEASTCHIPDB if you dodbmeta(dbconn(org.PfalciparumPlasmoDB.eg.db), "DBSCHEMA"), but you should get NOSCHEMADB for this OrgDb.Anyway, try fixing the IDs you use and if you get the same error, run
traceback()right after the error and post the output from that.Hi James, thank you very much for your reply.
Indeed my schema is NOSCHEMADB. On the other hand, the central identifier of my annotation package is ENTREZGID (it is mandatory for makeOrgPackage()) but the IDs I was passing to the function and the gene universe are gene symbols. I have changed both the gene universe and the passed IDs to ENTREZGIDs and the problem is still there though.
I attach the result of running traceback().