doc: update

NAMESPACE

@@ -77,9 +77,13 @@ export(anchors2)
 export(arrange)
 export(as_ginteractions)
 export(count)
+export(count_overlaps)
+export(count_overlaps_directed)
 export(end1)
 export(end2)
 export(filter)
+export(filter_by_non_overlaps)
+export(filter_by_overlaps)
 export(find_overlaps)
 export(find_overlaps_directed)
 export(flank_downstream)

R/count-overlaps.R

@@ -5,7 +5,7 @@
 #' When using `count_overlaps()` with a `PinnedGInteractions` object, 
 #' only the pinned anchors are used to check for overlap with `y`. 
 #' This is equivalent to specifying `use.region="both"` in 
-#' \code{\href{https://bioconductor.org/packages/release/bioc/vignettes/InteractionSet/inst/doc/interactions.html#27_Overlap_methods}{InteractionSet::countOverlaps()}}.
+#' `InteractionSet::findOverlaps()`.
 #' 
 #' @param x A (Pinned)GInteractions object
 #' @param y A GRanges object
@@ -81,7 +81,7 @@ count_overlaps.PinnedGInteractions <- function(
 #' @rdname ginteractions-count-overlaps
 #' @export
 count_overlaps.GInteractions <- function(
-    x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y")
+    x, y, maxgap = -1L, minoverlap = 0L
 ) {
 
     InteractionSet::countOverlaps( 
@@ -99,7 +99,7 @@ count_overlaps.GInteractions <- function(
 #' @rdname ginteractions-count-overlaps
 #' @export
 count_overlaps_directed.PinnedGInteractions <- function(
-    x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y")
+    x, y, maxgap = -1L, minoverlap = 0L
 ) {
 
     InteractionSet::countOverlaps( 
@@ -121,7 +121,7 @@ count_overlaps_directed.PinnedGInteractions <- function(
 #' @rdname ginteractions-count-overlaps
 #' @export
 count_overlaps_directed.GInteractions <- function(
-    x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y")
+    x, y, maxgap = -1L, minoverlap = 0L
 ) {
 
     InteractionSet::countOverlaps( 

R/filter-overlaps.R

@@ -5,7 +5,7 @@
 #' When using `filter_by_overlaps()` with a `PinnedGInteractions` object, 
 #' only the pinned anchors are used to check for overlap with `y`. 
 #' This is equivalent to specifying `use.region="both"` in 
-#' \code{\href{https://bioconductor.org/packages/release/bioc/vignettes/InteractionSet/inst/doc/interactions.html#27_Overlap_methods}{InteractionSet::countOverlaps()}}.
+#' `InteractionSet::findOverlaps()`.
 #' 
 #' @param x A (Pinned)GInteractions object
 #' @param y A GRanges object
@@ -81,7 +81,7 @@ filter_by_overlaps.PinnedGInteractions <- function(
 #' @rdname ginteractions-filter-overlaps
 #' @export
 filter_by_overlaps.GInteractions <- function(
-    x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y")
+    x, y, maxgap = -1L, minoverlap = 0L
 ) {
 
     IRanges::subsetByOverlaps( 
@@ -122,7 +122,7 @@ filter_by_non_overlaps.PinnedGInteractions <- function(
 #' @rdname ginteractions-filter-overlaps
 #' @export
 filter_by_non_overlaps.GInteractions <- function(
-    x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y")
+    x, y, maxgap = -1L, minoverlap = 0L
 ) {
 
     IRanges::subsetByOverlaps( 

R/find-overlaps.R

@@ -13,7 +13,7 @@
 #' When using `find_overlaps()` with a `PinnedGInteractions` object, 
 #' only the pinned anchors are used to check for overlap with `y`. 
 #' This is equivalent to specifying `use.region="both"` in 
-#' \code{\href{https://bioconductor.org/packages/release/bioc/vignettes/InteractionSet/inst/doc/interactions.html#27_Overlap_methods}{InteractionSet::findOverlaps()}}.
+#' `InteractionSet::findOverlaps()`.
 #' 
 #' @param x A (Pinned)GInteractions object
 #' @param y A GRanges object

R/reexports-plyranges.R

@@ -47,3 +47,23 @@ plyranges::find_overlaps
 #' @importFrom plyranges find_overlaps_directed
 #' @export
 plyranges::find_overlaps_directed
+
+#' @rdname reexports
+#' @importFrom plyranges count_overlaps
+#' @export
+plyranges::count_overlaps
+
+#' @rdname reexports
+#' @importFrom plyranges count_overlaps_directed
+#' @export
+plyranges::count_overlaps_directed
+
+#' @rdname reexports
+#' @importFrom plyranges filter_by_overlaps
+#' @export
+plyranges::filter_by_overlaps
+
+#' @rdname reexports
+#' @importFrom plyranges filter_by_non_overlaps
+#' @export
+plyranges::filter_by_non_overlaps