From 31c519be9f75ef8b71ddeb7c67750830c3d06352 Mon Sep 17 00:00:00 2001 From: hyginn Date: Sun, 4 Oct 2020 14:11:13 +1000 Subject: [PATCH] Bugfix: called the wrong function on ENSPsel in l. 220 --- BIN-PPI-Analysis.R | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/BIN-PPI-Analysis.R b/BIN-PPI-Analysis.R index daa4577..32c6159 100644 --- a/BIN-PPI-Analysis.R +++ b/BIN-PPI-Analysis.R @@ -4,12 +4,13 @@ # Purpose: A Bioinformatics Course: # 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) # # Versions: +# 1.3 Bugfix: called the wrong function on ENSPsel in l. 220 # 1.2 2020 Updates; Rewrite for new STRINg V11; # Deprecate save()/load() for saveRDS()/readRDS() # 1.1 Change from require() to requireNamespace(), @@ -32,7 +33,7 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> --------------------------------------------------------------- #TOC> 1 Setup and data 49 @@ -42,7 +43,7 @@ #TOC> 2.3 Betweenness Centrality 183 #TOC> 3 biomaRt 230 #TOC> 4 Task for submission 301 -#TOC> +#TOC> #TOC> ========================================================================== @@ -215,9 +216,9 @@ head(sBC) # 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: # 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... @@ -283,7 +284,7 @@ biomaRt::getBM(filters = "ensembl_peptide_id", 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. -for (ID in ENSPsel) { +for (ID in myENSPsel) { CPdefs[[ID]] <- biomaRt::getBM(filters = "ensembl_peptide_id", attributes = c("hgnc_symbol", "wikigene_description",