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hyginn 2020-09-25 13:20:10 +10:00
parent 5a3bbc31c6
commit abe30a5fb6
1 changed files with 12 additions and 16 deletions
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24
BIN-FUNC-Semantic_similarity.R
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@ -1,20 +1,15 @@
# tocID <- "BIN-FUNC_Semantic_similarity.R" # tocID <- "BIN-FUNC-Semantic_similarity.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
# #
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-FUNC_Semantic_similarity unit. # R code accompanying the BIN-FUNC_Semantic_similarity unit.
# #
# Version: 1.1 # Version: 1.2
# #
# Date: 2017 11 - 2019 01 # Date: 2017-11 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.2 2020 Maintenance
# 1.1 Change from require() to requireNamespace(), # 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout, # use <package>::<function>() idiom throughout,
# use Biocmanager:: not biocLite() # use Biocmanager:: not biocLite()
@ -37,10 +32,10 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------- #TOC> --------------------------------------------------------------------
#TOC> 1 Preparations: Packages, AnnotationDB, Setup 42 #TOC> 1 Preparations: Packages, AnnotationDB, Setup 43
#TOC> 2 Fetch GO Annotations 98 #TOC> 2 Fetch GO Annotations 100
#TOC> 3 Semantic Similarities 107 #TOC> 3 Semantic Similarities 109
#TOC> 4 GO Term Enrichment in Gene Sets 125 #TOC> 4 GO Term Enrichment in Gene Sets 127
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -68,7 +63,8 @@ if (! requireNamespace("GOSim", quietly = TRUE)) {
library(GOSim) library(GOSim)
# GOSim loads human annotations by default. We load yeast annotations instead... # GOSim loads human annotations in org.Hs.eg.db by default. We load yeast
# annotations instead...
if (! requireNamespace("org.Sc.sgd.db", quietly = TRUE)) { if (! requireNamespace("org.Sc.sgd.db", quietly = TRUE)) {
BiocManager::install("org.Sc.sgd.db") BiocManager::install("org.Sc.sgd.db")
} }