devtools::install_github("ericaenjoy3/GOplot")
library(GOplot)
Current available database: "C1.CYTO": positional gene sets; "C2.CGP": chemical and genetic perturbations; "C2.CP": Canonical pathways (including BioCarta, KEGG and Reactome gene sets); "C3.MIR": microRNA targets; "C3.TFT": transcription factor targets; "C4.CGN": cancer gene neighborhoods; "C4.CM": cancer modules; "C5.BP": GO biological process; "C5.CC": GO cellular component; "C5.MF": GO molecular function; "C6.ONCOGENE": oncogenic signatures; "C7.IMMUNE": immunologic signatures.
For example, to load canonical pathways
gset.obj <- selDB(major="C2.CP", minor="Reactome", type="symbols", species="mouse")
or to load gene ontology biological process
gset.obj <- selDB(major="C5.BP", minor=NA, type="symbols", species="mouse")
For example, prepare gene signatures to be tested
signatures=data.frame(gene = as.character(c("Nanog","Rpl3","Rpl4","Mbl2","Ubr1","Herc2","Asb4","Rnf123","Klf4","Uba5")),
clus = factor(rep(c('Group1','Group2'),c(6,4))))
gclus.obj <- new("gclus", tbl=tibble:::as_tibble(signatures))
res.list <- GO(gclus.obj, gset.obj, filterPADJ=FALSE, filterOR=TRUE)
go_set.obj <- res.list$go_set.obj
go_res.obj <- res.list$go_res.obj
write_GO(go_set.obj, go_res.obj, nms='test')
simi(go_set.obj, go_res.obj, nms='test')
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