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Update vector ID's for betweenness centrality

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hyginn 2020-10-21 06:13:36 +10:00
parent 052e148999
commit 08e1803c44
1 changed files with 13 additions and 12 deletions
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BIN-PPI-Analysis.R
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@ -4,12 +4,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PPI-Analysis unit. # R code accompanying the BIN-PPI-Analysis unit.
# #
# Version: 1.3 # Version: 1.4
# #
# Date: 2017-08 - 2020-10 # Date: 2017-08 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.4 Update vector ID's for betweenness centrality.
# 1.3 Bugfix: called the wrong function on ENSPsel in l. 220 # 1.3 Bugfix: called the wrong function on ENSPsel in l. 220
# 1.2 2020 Updates; Rewrite for new STRINg V11; # 1.2 2020 Updates; Rewrite for new STRINg V11;
# Deprecate save()/load() for saveRDS()/readRDS() # Deprecate save()/load() for saveRDS()/readRDS()
@ -32,17 +33,17 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------------------- #TOC> ---------------------------------------------------------------
#TOC> 1 Setup and data 49 #TOC> 1 Setup and data 50
#TOC> 2 Functional Edges in the Human Proteome 85 #TOC> 2 Functional Edges in the Human Proteome 86
#TOC> 2.1 Cliques 128 #TOC> 2.1 Cliques 129
#TOC> 2.2 Communities 169 #TOC> 2.2 Communities 170
#TOC> 2.3 Betweenness Centrality 183 #TOC> 2.3 Betweenness Centrality 184
#TOC> 3 biomaRt 230 #TOC> 3 biomaRt 231
#TOC> 4 Task for submission 301 #TOC> 4 Task for submission 302
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -201,8 +202,8 @@ names(BC$res) <- as.character(1:length(BC$res))
sBC <- sort(BC$res, decreasing = TRUE) sBC <- sort(BC$res, decreasing = TRUE)
head(sBC) head(sBC)
# This ordered vector means: node 3,862 has the highest betweeness centrality, # This ordered vector means: node 3 has the highest betweeness centrality,
# node 1,720 has the second highest.. etc. # node 721 has the second highest, etc.
(BCsel <- as.numeric(names(sBC)[1:10])) (BCsel <- as.numeric(names(sBC)[1:10]))