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Bugfix: called the wrong function on ENSPsel in l. 220

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hyginn 2020-10-04 14:11:13 +10:00
parent 285c0db8a5
commit 31c519be9f
1 changed files with 8 additions and 7 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: 1.2 # Version: 1.3
# #
# Date: 2017-08 - 2020-09 # Date: 2017-08 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 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()
# 1.1 Change from require() to requireNamespace(), # 1.1 Change from require() to requireNamespace(),
@ -32,7 +33,7 @@
#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 49
@ -42,7 +43,7 @@
#TOC> 2.3 Betweenness Centrality 183 #TOC> 2.3 Betweenness Centrality 183
#TOC> 3 biomaRt 230 #TOC> 3 biomaRt 230
#TOC> 4 Task for submission 301 #TOC> 4 Task for submission 301
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -215,9 +216,9 @@ head(sBC)
# IMPORTANT, IF YOU INTEND TO SUBMIT YOUR ANALYSIS FOR CREDIT # IMPORTANT, IF YOU INTEND TO SUBMIT YOUR ANALYSIS FOR CREDIT
# We are going to use these IDs to produce some output for a submitted task: # We are going to use these IDs to produce some output for a submitted task:
# therefore I need you to execute the following line, note the "seal" that this # therefore I need you to execute the following line, note the "seal" that this
# returns, and not change ENSPsel later: # returns, and not change myENSPsel later:
myENSPsel <- seal(ENSPsel) myENSPsel <- selectENSP(ENSPsel)
# Next, to find what these proteins are... # Next, to find what these proteins are...
@ -283,7 +284,7 @@ biomaRt::getBM(filters = "ensembl_peptide_id",
CPdefs <- list() # Since we don't know how many matches one of our queries CPdefs <- list() # Since we don't know how many matches one of our queries
# will return, we'll put the result dataframes into a list. # will return, we'll put the result dataframes into a list.
for (ID in ENSPsel) { for (ID in myENSPsel) {
CPdefs[[ID]] <- biomaRt::getBM(filters = "ensembl_peptide_id", CPdefs[[ID]] <- biomaRt::getBM(filters = "ensembl_peptide_id",
attributes = c("hgnc_symbol", attributes = c("hgnc_symbol",
"wikigene_description", "wikigene_description",