@@ -38,7 +38,8 @@ expand.CoverageExperiment <- function(data, ..., .name_repair = NULL) {

             m <- assay(data, "coverage")[f, t][[1]] |> 

                 as.data.frame() |>

                 dplyr::mutate(

-                    track = t, features = f, 

+                    track = factor(t, levels = tracks), 

+                    features = factor(f, levels = features), 

                     chr = as.vector(seqnames(rr)), 

                     ranges = as.character(rr), 

                     strand = as.vector(strand(rr))

@@ -12,7 +12,7 @@

 #' @aliases expand,CoverageExperiment-method

 #' @rdname expand

 #' 

-#' @param x a `CoverageExperiment` object

+#' @param data a `CoverageExperiment` object

 #' @param ...,.name_repair ignored

 #' @return a `tibble` object

 #' 

@@ -24,18 +24,18 @@

 #' 

 #' expand(ce)

-expand.CoverageExperiment <- function(x, ..., .name_repair = NULL) {

-    tracks <- colData(x)$track

-    features <- rowData(x)$features

-    w <- width(rowRanges(x)[[1]])[[1]]

-    bin <- w / ncol(assay(x, "coverage")[1, 1][[1]])

+expand.CoverageExperiment <- function(data, ..., .name_repair = NULL) {

+    tracks <- colData(data)$track

+    features <- rowData(data)$features

+    w <- width(rowRanges(data)[[1]])[[1]]

+    bin <- w / ncol(assay(data, "coverage")[1, 1][[1]])

     df <- lapply(features, function(f) {

-        rr <- rowRanges(x)[[f]]

+        rr <- rowRanges(data)[[f]]

         rrdf <- as.data.frame(rr)

         coord <- lapply(seq_len(nrow(rrdf)), function(K) seq(rrdf[K, 'start'], rrdf[K, 'end'], by = bin)) |> unlist()

         coord.scaled <- lapply(seq_len(nrow(rrdf)), function(K) seq(-w/2, w/2-1, by = bin)) |> unlist()

         lapply(tracks, function(t) {

-            m <- assay(x, "coverage")[f, t][[1]] |> 

+            m <- assay(data, "coverage")[f, t][[1]] |> 

                 as.data.frame() |>

                 dplyr::mutate(

                     track = t, features = f, 

@@ -55,7 +55,7 @@ expand.CoverageExperiment <- function(x, ..., .name_repair = NULL) {

         }) |> dplyr::bind_rows()

     }) |> 

         dplyr::bind_rows() |> 

-        dplyr::left_join(colData(x) |> as.data.frame(), by = 'track') |> 

+        dplyr::left_join(colData(data) |> as.data.frame(), by = 'track') |> 

         dplyr::group_by(track, features, ranges)

     return(df)

 }

@@ -13,10 +13,10 @@

 #' @rdname expand

 #' 

 #' @param x a `CoverageExperiment` object

-#' @param ... ignored

+#' @param ...,.name_repair ignored

 #' @return a `tibble` object

 #' 

-#' @importFrom S4Vectors expand

+#' @importFrom tidyr expand

 #' @export

 #' @examples 

 #' data(ce)

@@ -24,7 +24,7 @@

 #' 

 #' expand(ce)

-setMethod("expand", signature(x = "CoverageExperiment"), function(x, ...) {

+expand.CoverageExperiment <- function(x, ..., .name_repair = NULL) {

     tracks <- colData(x)$track

     features <- rowData(x)$features

     w <- width(rowRanges(x)[[1]])[[1]]

@@ -33,6 +33,7 @@ setMethod("expand", signature(x = "CoverageExperiment"), function(x, ...) {

         rr <- rowRanges(x)[[f]]

         rrdf <- as.data.frame(rr)

         coord <- lapply(seq_len(nrow(rrdf)), function(K) seq(rrdf[K, 'start'], rrdf[K, 'end'], by = bin)) |> unlist()

+        coord.scaled <- lapply(seq_len(nrow(rrdf)), function(K) seq(-w/2, w/2-1, by = bin)) |> unlist()

         lapply(tracks, function(t) {

             m <- assay(x, "coverage")[f, t][[1]] |> 

                 as.data.frame() |>

@@ -45,10 +46,11 @@ setMethod("expand", signature(x = "CoverageExperiment"), function(x, ...) {

                 dplyr::relocate(tidyr::all_of(c("track", "features", "chr", "ranges", "strand")))

             d <- tidyr::pivot_longer(

                 m, 

-                !tidyr::any_of(c("track", "features", "chr", "ranges", "strand")), 

+                !tidyr::any_of(c("track", "features", "chr", "ranges", "strand", "coord.scaled")), 

                 names_to = "coord", values_to = "coverage"

             )

             d$coord <- coord

+            d$coord.scaled <- coord.scaled

             d

         }) |> dplyr::bind_rows()

     }) |> 

@@ -56,4 +58,4 @@ setMethod("expand", signature(x = "CoverageExperiment"), function(x, ...) {

         dplyr::left_join(colData(x) |> as.data.frame(), by = 'track') |> 

         dplyr::group_by(track, features, ranges)

     return(df)

-})

+}

@@ -8,7 +8,7 @@

 #' object into a long data frame, and adds the `ranges` 

 #' and `seqnames` to the resulting `tibble`. 

 #' 

-#' @name expand

+#' @name expand,CoverageExperiment

 #' @aliases expand,CoverageExperiment-method

 #' @rdname expand

 #' 

@@ -1,4 +1,12 @@

-#' expand 

+#' Expand a CoverageExperiment object

+#' 

+#' @description

+#' A `CoverageExperiment` object can be coerced into a `tibble` using the 

+#' `tidySummarizedExperiment` package, but this will not turn 

+#' each coverage matrix into a "long" format. The `expand` function 

+#' provided here allows one to coerce a `CoverageExperiment`

+#' object into a long data frame, and adds the `ranges` 

+#' and `seqnames` to the resulting `tibble`. 

 #' 

 #' @name expand

 #' @aliases expand,CoverageExperiment-method

new file mode 100644

@@ -0,0 +1,51 @@

+#' expand 

+#' 

+#' @name expand

+#' @aliases expand,CoverageExperiment-method

+#' @rdname expand

+#' 

+#' @param x a `CoverageExperiment` object

+#' @param ... ignored

+#' @return a `tibble` object

+#' 

+#' @importFrom S4Vectors expand

+#' @export

+#' @examples 

+#' data(ce)

+#' ce

+#' 

+#' expand(ce)

+

+setMethod("expand", signature(x = "CoverageExperiment"), function(x, ...) {

+    tracks <- colData(x)$track

+    features <- rowData(x)$features

+    w <- width(rowRanges(x)[[1]])[[1]]

+    bin <- w / ncol(assay(x, "coverage")[1, 1][[1]])

+    df <- lapply(features, function(f) {

+        rr <- rowRanges(x)[[f]]

+        rrdf <- as.data.frame(rr)

+        coord <- lapply(seq_len(nrow(rrdf)), function(K) seq(rrdf[K, 'start'], rrdf[K, 'end'], by = bin)) |> unlist()

+        lapply(tracks, function(t) {

+            m <- assay(x, "coverage")[f, t][[1]] |> 

+                as.data.frame() |>

+                dplyr::mutate(

+                    track = t, features = f, 

+                    chr = as.vector(seqnames(rr)), 

+                    ranges = as.character(rr), 

+                    strand = as.vector(strand(rr))

+                ) |> 

+                dplyr::relocate(tidyr::all_of(c("track", "features", "chr", "ranges", "strand")))

+            d <- tidyr::pivot_longer(

+                m, 

+                !tidyr::any_of(c("track", "features", "chr", "ranges", "strand")), 

+                names_to = "coord", values_to = "coverage"

+            )

+            d$coord <- coord

+            d

+        }) |> dplyr::bind_rows()

+    }) |> 

+        dplyr::bind_rows() |> 

+        dplyr::left_join(colData(x) |> as.data.frame(), by = 'track') |> 

+        dplyr::group_by(track, features, ranges)

+    return(df)

+})