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Cope with GenomicFeatures update after BioC 3.13 #21

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f36e9e4
Cope with GenomicFeatures update
Tim-Yu Aug 25, 2022
0504e83
Update README.md
Tim-Yu Sep 7, 2022
ea8ccf9
Change install to usr lib for lower permission
Tim-Yu Sep 7, 2022
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14 changes: 9 additions & 5 deletions R/orfquant.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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))

Expand Down Expand Up @@ -3536,7 +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 = ""))


Expand Down Expand Up @@ -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



Expand Down Expand Up @@ -5984,4 +5988,4 @@ plot_orfquant_locus<-function(locus,orfquant_results,bam_files, plotfile='locusp
normalizePath(plotfile)
#return file name
return(plotfile)
}
}
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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")

Expand Down