From 9e704e42a85407fa71410502c071d02d4a52dc39 Mon Sep 17 00:00:00 2001 From: Holger Brandl Date: Wed, 6 Sep 2017 13:35:06 +0200 Subject: [PATCH] started impl of cp_enrichment for yeast --- R/bio/cp_utils.R | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/R/bio/cp_utils.R b/R/bio/cp_utils.R index a40543c..2460dd4 100644 --- a/R/bio/cp_utils.R +++ b/R/bio/cp_utils.R @@ -1,7 +1,7 @@ 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 -- GitLab