feat: new getters anchors{12} ranges{12}

NAMESPACE

@@ -8,12 +8,16 @@ S3method(filter,GInteractions)
 S3method(mutate,GInteractions)
 S3method(select,GInteractions)
 S3method(slice,GInteractions)
+export(anchors1)
+export(anchors2)
 export(arrange)
 export(as_ginteractions)
 export(end1)
 export(end2)
 export(filter)
 export(mutate)
+export(ranges1)
+export(ranges2)
 export(select)
 export(seqnames1)
 export(seqnames2)
@@ -25,8 +29,12 @@ export(strand2)
 export(width1)
 export(width2)
 exportMethods("$")
+exportMethods(anchors1)
+exportMethods(anchors2)
 exportMethods(end1)
 exportMethods(end2)
+exportMethods(ranges1)
+exportMethods(ranges2)
 exportMethods(seqnames1)
 exportMethods(seqnames2)
 exportMethods(start1)
@@ -39,14 +47,19 @@ importFrom(BiocGenerics,end)
 importFrom(BiocGenerics,start)
 importFrom(BiocGenerics,strand)
 importFrom(BiocGenerics,width)
+importFrom(GenomeInfoDb,seqinfo)
 importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomicRanges,GRanges)
 importFrom(IRanges,IRanges)
+importFrom(IRanges,ranges)
 importFrom(InteractionSet,GInteractions)
+importFrom(InteractionSet,anchors)
+importFrom(InteractionSet,regions)
 importFrom(S4Vectors,"first<-")
 importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,"second<-")
 importFrom(S4Vectors,mcols)
+importFrom(S4Vectors,showAsCell)
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)

R/ginteractions-getters.R

@@ -10,8 +10,10 @@
 #' @examples 
 #' gi <- data.frame(
 #'   seqnames1 = 'chr1', start1 = 1, end1 = 10, 
-#'   seqnames2 = 'chr1', start2 = 1, end2 = 10
+#'   seqnames2 = 'chr1', start2 = 2, end2 = 20
 #' ) |> as_ginteractions() |> mutate(type = 'cis')
+#' anchors1(gi)
+#' anchors2(gi)
 #' seqnames1(gi)
 #' seqnames2(gi)
 #' start1(gi)
@@ -20,6 +22,8 @@
 #' end2(gi)
 #' width1(gi)
 #' width2(gi)
+#' ranges1(gi)
+#' ranges2(gi)
 #' strand1(gi)
 #' strand2(gi)
 #' gi$type
@@ -37,6 +41,12 @@ setMethod("$", "GInteractions",
     function(x, name) mcols(x, use.names=FALSE)[[name]]
 )
 
+#' @rdname ginteractions-getters
+#' @export
+setGeneric("anchors1", function(x) standardGeneric("anchors1"))
+#' @rdname ginteractions-getters
+#' @export
+setGeneric("anchors2", function(x) standardGeneric("anchors2"))
 #' @rdname ginteractions-getters
 #' @export
 setGeneric("seqnames1", function(x) standardGeneric("seqnames1"))
@@ -67,58 +77,86 @@ setGeneric("strand1", function(x) standardGeneric("strand1"))
 #' @rdname ginteractions-getters
 #' @export
 setGeneric("strand2", function(x) standardGeneric("strand2"))
+#' @rdname ginteractions-getters
+#' @export
+setGeneric("ranges1", function(x) standardGeneric("ranges1"))
+#' @rdname ginteractions-getters
+#' @export
+setGeneric("ranges2", function(x) standardGeneric("ranges2"))
+
+#' @rdname ginteractions-getters
+#' @export
+setMethod("anchors1", signature("GInteractions"), function(x) {
+    S4Vectors::first(x)
+})
+#' @rdname ginteractions-getters
+#' @export
+setMethod("anchors2", signature("GInteractions"), function(x) {
+    S4Vectors::second(x)
+})
 #' @importFrom GenomeInfoDb seqnames
 #' @rdname ginteractions-getters
 #' @export
 setMethod("seqnames1", signature("GInteractions"), function(x) {
-    GenomeInfoDb::seqnames(S4Vectors::first(x))
+    GenomeInfoDb::seqnames(anchors1(x))
 })
 #' @rdname ginteractions-getters
 #' @export
 setMethod("seqnames2", signature("GInteractions"), function(x) {
-    GenomeInfoDb::seqnames(S4Vectors::second(x))
+    GenomeInfoDb::seqnames(anchors2(x))
 })
 #' @importFrom BiocGenerics start
 #' @rdname ginteractions-getters
 #' @export
 setMethod("start1", signature("GInteractions"), function(x) {
-    BiocGenerics::start(S4Vectors::first(x))
+    BiocGenerics::start(anchors1(x))
 })
 #' @rdname ginteractions-getters
 #' @export
 setMethod("start2", signature("GInteractions"), function(x) {
-    BiocGenerics::start(S4Vectors::second(x))
+    BiocGenerics::start(anchors2(x))
 })
 #' @importFrom BiocGenerics end
 #' @rdname ginteractions-getters
 #' @export
 setMethod("end1", signature("GInteractions"), function(x) {
-    BiocGenerics::end(S4Vectors::first(x))
+    BiocGenerics::end(anchors1(x))
 })
 #' @rdname ginteractions-getters
 #' @export
 setMethod("end2", signature("GInteractions"), function(x) {
-    BiocGenerics::end(S4Vectors::second(x))
+    BiocGenerics::end(anchors2(x))
 })
 #' @importFrom BiocGenerics width
 #' @rdname ginteractions-getters
 #' @export
 setMethod("width1", signature("GInteractions"), function(x) {
-    BiocGenerics::width(S4Vectors::first(x))
+    BiocGenerics::width(anchors1(x))
 })
 #' @rdname ginteractions-getters
 #' @export
 setMethod("width2", signature("GInteractions"), function(x) {
-    BiocGenerics::width(S4Vectors::second(x))
+    BiocGenerics::width(anchors2(x))
 })
 #' @importFrom BiocGenerics strand
 #' @rdname ginteractions-getters
 #' @export
 setMethod("strand1", signature("GInteractions"), function(x) {
-    BiocGenerics::strand(S4Vectors::first(x))
+    BiocGenerics::strand(anchors1(x))
 })
 #' @rdname ginteractions-getters
 #' @export
 setMethod("strand2", signature("GInteractions"), function(x) {
-    BiocGenerics::strand(S4Vectors::second(x))
+    BiocGenerics::strand(anchors2(x))
+})
+#' @importFrom IRanges ranges
+#' @rdname ginteractions-getters
+#' @export
+setMethod("ranges1", signature("GInteractions"), function(x) {
+    IRanges::ranges(anchors1(x))
+})
+#' @rdname ginteractions-getters
+#' @export
+setMethod("ranges2", signature("GInteractions"), function(x) {
+    IRanges::ranges(anchors2(x))
 })

README.md

@@ -20,6 +20,8 @@ and logical expressions;
 - Pick out any columns from the associated metadata with `select` 
 using [`<tidy-select>` arguments](https://dplyr.tidyverse.org/reference/dplyr_tidy_select.html); 
 - Subset using indices with `slice`. 
+- Order genomic interactions with `arrange` using categorical/numerical 
+variables. 
 
 ## Installation
 
@@ -42,4 +44,4 @@ This package is largely inspired by `plyranges` and the `tidyverse`:
 
 - Lee, Stuart, Dianne Cook, and Michael Lawrence. 2019. “Plyranges: A Grammar of Genomic Data Transformation.” Genome Biology 20 (1): 4. https://doi.org/10.1186/s13059-018-1597-8.
 - Wickham H, François R, Henry L, Müller K, Vaughan D (2023). _dplyr: A Grammar of Data Manipulation_. R package version 1.1.2, <https://CRAN.R-project.org/package=dplyr>.
-- Henry L, Wickham H (2023). _rlang: Functions for Base Types and Core R and 'Tidyverse' Features_. R package version 1.1.1, <https://CRAN.R-project.org/package=rlang>.
+- Henry L, Wickham H (2023). _rlang: Functions for Base Types and Core R and 'Tidyverse' Features_. R package version 1.1.1, <https://CRAN.R-project.org/package=rlang>.