From f36e9e464659cb26c4d32b3acd28d20878f3b042 Mon Sep 17 00:00:00 2001 From: Tim Yu Date: Thu, 25 Aug 2022 15:32:06 +0100 Subject: [PATCH 1/3] Cope with GenomicFeatures update disjointExons is deprecated, so use exonicParts instead and mimic back to the disjoint format --- R/orfquant.R | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/R/orfquant.R b/R/orfquant.R index f96f84e..977e65f 100644 --- a/R/orfquant.R +++ b/R/orfquant.R @@ -1212,8 +1212,9 @@ select_quantify_ORFs<-function(results_ORFs,P_sites,P_sites_uniq,cutoff_cums=NA, #disjointExons(orfann) - exbin<-disjointExons(orfann) - + # exbin<-disjointExons(orfann) + exbin<-exonicParts(orfann,linked.to.single.gene.only = T) #disjointExons is deprecated, so use exonicParts instead and mimic back to the disjoint format + mcols(exbin) <- mcols(exbin)[,c(3,2,7)] d<-rep(0,length(exbin)) @@ -3616,7 +3617,10 @@ prepare_annotation_files<-function(annotation_directory,twobit_file=NULL,gtf_fil #define exonic bins, including regions overlapping multiple genes - nsns<-disjointExons(annotation,aggregateGenes=T) + + #nsns<-disjointExons(annotation,aggregateGenes=T) + nsns<-exonicParts(annotation, linked.to.single.gene.only=F) + mcols(nsns) <- DataFrame(mcols(nsns)[c(3,2)],exonic_part=NA) #disjointExons is deprecated, so use exonicParts instead and mimic back to the disjoint format @@ -5984,4 +5988,4 @@ plot_orfquant_locus<-function(locus,orfquant_results,bam_files, plotfile='locusp normalizePath(plotfile) #return file name return(plotfile) -} \ No newline at end of file +} From 0504e83590bbea68d1a46b5a1096950f5785499a Mon Sep 17 00:00:00 2001 From: Tim Yu Date: Wed, 7 Sep 2022 09:47:32 +0100 Subject: [PATCH 2/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 76d58c2..f0da8d0 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ To install *ORFquant*: ``` library("devtools") -install_github(repo = "lcalviell/ORFquant") +install_github(repo = "Tim-Yu/ORFquant") # until they merge library("ORFquant") From ea8ccf9d9b1f92c7253700d7fa60fd26dc9dcb23 Mon Sep 17 00:00:00 2001 From: Tim Yu Date: Wed, 7 Sep 2022 14:07:20 +0100 Subject: [PATCH 3/3] Change install to usr lib for lower permission --- R/orfquant.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/orfquant.R b/R/orfquant.R index 977e65f..e9bdf66 100644 --- a/R/orfquant.R +++ b/R/orfquant.R @@ -3537,7 +3537,7 @@ prepare_annotation_files<-function(annotation_directory,twobit_file=NULL,gtf_fil cat(paste("Installing the BSgenome package ... ",date(),"\n",sep = "")) - install(paste(annotation_directory,pkgnm,sep="/"),upgrade = F) + install(paste(annotation_directory,pkgnm,sep="/"),upgrade = F,library=.libPaths()[1],lib=.libPaths()[1]) cat(paste("Installing the BSgenome package --- Done! ",date(),"\n",sep = ""))