Commit 9e704e42 authored by Holger Brandl's avatar Holger Brandl

started impl of cp_enrichment for yeast

parent 4ea24c72
install_package("clusterProfiler")
## todo move to diffex commons
## species names according to http://www.genome.jp/kegg/catalog/org_list.html
guess_cp_species <- function(ensIds){
an_id <-ensIds[1]
......@@ -18,6 +18,8 @@ guess_cp_species <- function(ensIds){
}
}
## todo how to guess yeast ("org.Sc.sgd.db") from id?
guess_anno_db <- function(ensIds){
an_id <-ensIds[1]
......@@ -34,11 +36,13 @@ guess_anno_db <- function(ensIds){
}
}
## see http://bioconductor.org/packages/release/BiocViews.html#___OrgDb
#source("http://bioconductor.org/biocLite.R")
#biocLite("org.Mm.eg.db")
#biocLite("org.Hs.eg.db")
#biocLite("org.Dr.eg.db")
#biocLite("org.Dm.eg.db")
#biocLite("org.Sc.sgd.db")
#biocLite("KEGG.db")
#biocLite("ReactomePA")
......@@ -61,6 +65,8 @@ find_enr_terms = function(ensemblIds, ...){
# quote({find_enr_terms(ensemblIds, ...)}) %>% cache_it(paste0("cp_id_cache", digest(ensemblIds)))
#}
#' TODO remove necessity for cp_species
geneIds = glMapped %>% first() %>% pull(entrez_gene_id)
cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
# DEBUG geneIds <- glMapped %>% filter(cluster %in% c("cluster_9")) %$% entrez_gene_id %>% as.integer
......
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