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

upgrade

parent f3056ace
......@@ -13,6 +13,7 @@ Imports:
IRanges,
methods,
plotly,
rtracklayer,
UpSetR
Suggests:
BiocStyle,
......
......@@ -38,3 +38,4 @@ importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(rtracklayer,import)
......@@ -4,7 +4,7 @@
#' @importFrom AnnotationDbi select keys as.data.frame metadata
#' @importFrom GenomicFeatures promoters transcripts fiveUTRsByTranscript threeUTRsByTranscript exonsBy intronsByTranscript cdsBy
#' @importFrom GenomicRanges flank
#' @importFrom rtracklayer import
#' @importFrom rtracklayer import
#' @importFrom BiocGenerics as.data.frame
#' @importFrom methods new
#' @import data.table
......
......@@ -64,7 +64,7 @@ setMethod("show", "genome_features",function(object) {
###################
# count genes
genes<-base::length(base::unique(gene_table$GeneID))
genes<-base::length(base::unique(gene_table$gene_id))
###################
# count
......
......@@ -223,7 +223,15 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
###################
# 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{
###################
......
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