genome_feaures_overlaps update

R/genome_features_overlaps.R

@@ -10,8 +10,7 @@
 #' @importFrom UpSetR upset
 #' @import data.table
 #' @param peaks a  \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.
-#' @param features a \code{\link[base]{vector}} of features \code{\link[base]{character}} with by
-#' default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron", "cds", and "downstream").
+#' @param features a \code{\link{genome_features-class}} object.
 #' @param figs_path the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).
 #' @param ignore.strand ignore peak coordinate orientation (defaul to TRUE).
 #' @details This method build a convenient genomic features object, in order to be used for finding overlaps beetween
@@ -25,12 +24,12 @@
 #'  peaks,
 #'  features,
 #'  figs_path="./data/output/",
-#'  ignore.strand = T
+#'  ignore.strand = TRUE
 #' )
 #' @name genome_features_overlaps
 #' @rdname genome_features_overlaps-methods
 #' @exportMethod genome_features_overlaps
-setGeneric(name="genome_features_overlaps",def=function(peaks,features=base::c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),figs_path="./data/figs/",ignore.strand=TRUE){
+setGeneric(name="genome_features_overlaps",def=function(peaks,features,figs_path="./data/figs/",ignore.strand=TRUE){
   standardGeneric("genome_features_overlaps")
 })
 
@@ -39,7 +38,8 @@ setGeneric(name="genome_features_overlaps",def=function(peaks,features=base::c("
 setMethod(
   "genome_features_overlaps",
   methods::signature(
-    peaks="list"
+    peaks="CompressedGRangesList",
+    features="genome_features"
   ),
   definition=function(peaks,features,figs_path,ignore.strand){
 

man/genome_features_overlaps-methods.Rd

@@ -3,22 +3,20 @@
 \docType{methods}
 \name{genome_features_overlaps}
 \alias{genome_features_overlaps}
-\alias{genome_features_overlaps,list-method}
+\alias{genome_features_overlaps,CompressedGRangesList,genome_features-method}
 \title{find overlaps between genomic coordinates and features.}
 \usage{
-genome_features_overlaps(peaks, features = base::c("promoter", "UTR5",
-  "UTR3", "exon", "intron", "cds", "downstream"),
-  figs_path = "./data/figs/", ignore.strand = TRUE)
+genome_features_overlaps(peaks, features, figs_path = "./data/figs/",
+  ignore.strand = TRUE)
 
-\S4method{genome_features_overlaps}{list}(peaks,
-  features = base::c("promoter", "UTR5", "UTR3", "exon", "intron", "cds",
-  "downstream"), figs_path = "./data/figs/", ignore.strand = TRUE)
+
+  \S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(peaks,
+  features, figs_path = "./data/figs/", ignore.strand = TRUE)
 }
 \arguments{
 \item{peaks}{a  \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.}
 
-\item{features}{a \code{\link[base]{vector}} of features \code{\link[base]{character}} with by
-default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron", "cds", and "downstream").}
+\item{features}{a \code{\link{genome_features-class}} object.}
 
 \item{figs_path}{the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).}
 
@@ -40,6 +38,6 @@ features_overlaps<-GenomeFeatures::genome_features_overlaps(
  peaks,
  features,
  figs_path="./data/output/",
- ignore.strand = T
+ ignore.strand = TRUE
 )
 }