Commit 586c30ba authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

upgrade

parent f3056ace
...@@ -13,6 +13,7 @@ Imports: ...@@ -13,6 +13,7 @@ Imports:
IRanges, IRanges,
methods, methods,
plotly, plotly,
rtracklayer,
UpSetR UpSetR
Suggests: Suggests:
BiocStyle, BiocStyle,
......
...@@ -38,3 +38,4 @@ importFrom(methods,slot) ...@@ -38,3 +38,4 @@ importFrom(methods,slot)
importFrom(methods,slotNames) importFrom(methods,slotNames)
importFrom(plotly,layout) importFrom(plotly,layout)
importFrom(plotly,plot_ly) importFrom(plotly,plot_ly)
importFrom(rtracklayer,import)
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
#' @importFrom AnnotationDbi select keys as.data.frame metadata #' @importFrom AnnotationDbi select keys as.data.frame metadata
#' @importFrom GenomicFeatures promoters transcripts fiveUTRsByTranscript threeUTRsByTranscript exonsBy intronsByTranscript cdsBy #' @importFrom GenomicFeatures promoters transcripts fiveUTRsByTranscript threeUTRsByTranscript exonsBy intronsByTranscript cdsBy
#' @importFrom GenomicRanges flank #' @importFrom GenomicRanges flank
#' @importFrom rtracklayer import #' @importFrom rtracklayer import
#' @importFrom BiocGenerics as.data.frame #' @importFrom BiocGenerics as.data.frame
#' @importFrom methods new #' @importFrom methods new
#' @import data.table #' @import data.table
......
...@@ -64,7 +64,7 @@ setMethod("show", "genome_features",function(object) { ...@@ -64,7 +64,7 @@ setMethod("show", "genome_features",function(object) {
################### ###################
# count genes # count genes
genes<-base::length(base::unique(gene_table$GeneID)) genes<-base::length(base::unique(gene_table$gene_id))
################### ###################
# count # count
......
...@@ -223,7 +223,15 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat ...@@ -223,7 +223,15 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
################### ###################
# merge with overlapped features # merge with overlapped features
annot<-merge(annot,features@gene_table,by.x="tx_name",by.y="Name",all.x=T,sort=F) annot<-merge(
annot,
features@gene_table[,.(type,gene_name,transcript_id,gene_id)],
by.x="tx_name",
by.y="transcript_id",
all.x=T,
sort=F
)
}else{ }else{
################### ###################
......
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