Commit 237df4c2 authored by Holger Brandl's avatar Holger Brandl

started impl of cp_enrichment for yeast

parent 95075a46
......@@ -19,13 +19,13 @@ Options:
opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
coreCommons = "https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/core_commons.R"
coreCommons = "https://raw.githubusercontent.com/holgerbrandl/datautils/v1.43/R/core_commons.R"
devtools::source_url(coreCommons)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/ggplot_commons.R")
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/cp_utils.R")
devtools::source_url("https://www.dropbox.com/s/p2b8luxf7jteb63/cp_utils.R?dl=1")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/diffex_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.43/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.43/R/bio/cp_utils.R")
# devtools::source_url("https://www.dropbox.com/s/p2b8luxf7jteb63/cp_utils.R?dl=1")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.43/R/bio/diffex_commons.R")
load_pack(knitr)
load_pack(DT)
......@@ -86,6 +86,8 @@ geneLists %>%
cp_species <- guess_cp_species(geneLists$ensembl_gene_id)
annoDb <- guess_anno_db(geneLists$ensembl_gene_id) # e.g. "org.Hs.eg.db"
# cp_species <- "sce"
# annoDb <- "org.Sc.sgd.db"
## supported ids
#idType("org.Hs.eg.db")
......@@ -136,8 +138,8 @@ cache_it(paste0("enrdata_", digest(glMapped)))
# add information on GO levels:
library(clusterProfiler)
library(goProfiles)
load_pack(clusterProfiler)
load_pack(goProfiles)
getlevels <- function(x){
dbs <- x %>% filter(grepl("go_", ontology)) %>% mutate(GOs = str_replace(ontology, "go_", ""))
......
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