Hi I am new to clusterprofiler and R. I have read the vignette also. I could use the groupGO easily on the set of genes but enrichGO throws an error saying "Error in enrichGO(gene = cephalexinlist, organism = "ecolik12", ont = "BP", : unused argument (organism = "ecolik12")". The script is below.
What am I doing wrong here? Please any help will be appreciated. Many thanks in advance.
library(clusterProfiler)
list<-c("947767", "947672", "947507", "945554", "946343", "945972", "945947", "946526", "944968", "948848", "948661", "945059", "948650", "946185", "947449", "948698", "945278", "947095", "948665", "945957", "947019", "946107", "946243", "944797", "946677", "948666", "946053", "948150", "947189", "948566")
enrichedgo <- enrichGO(list, organism="ecolik12", ont = "BP", pvalueCutoff = 0.05, readable = TRUE)
>sessioninfo()
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:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.EcK12.eg.db_3.5.0 GO.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0
[6] Biobase_2.38.0 BiocGenerics_0.24.0 xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-9
[11] BiocInstaller_1.28.0 clusterProfiler_3.6.0 DOSE_3.4.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
DESCRIPTION file of package 'Rcpp' is missing or broken
> traceback()
7: FUN(X[[i]], ...)
6: lapply(X = X, FUN = FUN, ...)
5: sapply(L[[n]], function(x) x[["Version"]])
4: mkLabel(x, "loadedOnly")
3: print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
2: print.sessionInfo(x)
1: function (x, ...)
UseMethod("print")(x)
