Ran github actions

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: extraChIPs
-Version: 1.7.6
+Version: 1.7.7
 Title: Additional functions for working with ChIP-Seq data
 Authors@R: person("Stevie", "Pederson", 
   email = "[email protected]", 

NEWS.md

@@ -100,4 +100,8 @@
 
 # Changes in 1.7.6
 
-- Added the DESeq2 Wald statistic to options for fitAssayDiff
+- Added the DESeq2 Wald statistic to options for `fitAssayDiff()`
+
+# Changes in 1.7.7
+
+- Added `merge_within` to `makeConsensus()` for better handling when `method = "coverage"`

R/makeConsensus.R

@@ -11,10 +11,10 @@
 #' range which are 'covered' by the minimum proportion of replicates specified
 #' are returned. This will return narrower peaks in general, although some
 #' artefactual very small ranges may be included (e.g. 10bp). Careful setting
-#' of the min_width parameter may be very helpful for these instances. It is
-#' also expected that setting method = "coverage" should return the region
-#' within each range which is more likely to contain the true binding site for
-#' the relevant ChIP targets
+#' of the min_width and merge_within parameters may be very helpful for these
+#' instances. It is also expected that setting method = "coverage" should return
+#' the region within each range which is more likely to contain the true binding
+#'  site for the relevant ChIP targets
 #'
 #'
 #' @param x A GRangesList
@@ -29,6 +29,7 @@
 #' @param ignore.strand,simplify,... Passed to \link{reduceMC} or
 #' \link{intersectMC} internally
 #' @param min_width Discard any regions below this width
+#' @param merge_within Passed to \link[GenomicRanges]{reduce} as `min.gapwidth`
 #'
 #' @return
 #' `GRanges` object with mcols containing a logical vector for every element of
@@ -60,7 +61,8 @@
 #' @export
 makeConsensus <- function(
         x, p = 0, var = NULL, method = c("union", "coverage"),
-        ignore.strand = TRUE, simplify = FALSE, min_width = 0, ...
+        ignore.strand = TRUE, simplify = FALSE, min_width = 0,
+        merge_within = 1L, ...
 ) {
 
     ## Starting with a GRList
@@ -91,22 +93,32 @@ makeConsensus <- function(
         cov_gr <- GRanges(coverage(x))
         cov_gr <- subsetByOverlaps(cov_gr, unlisted)
         ## Coverage will be returned as the column 'score'
-        cov_gr <- cov_gr[mcols(cov_gr)[["score"]] >= p * length(x)]
+        keep <- mcols(cov_gr)[["score"]] >= p * length(x)
+        cov_gr <- cov_gr[keep]
+        ## If merging within a certain range, merge here. This ensures that
+        ## returned regions still have coverage but deals with small holes
+        ## that appear due to drops in coverage, without messing up the *MC
+        cov_gr <- GenomicRanges::reduce(
+            cov_gr, min.gapwidth = merge_within, ignore.strand = ignore.strand
+        )
         red_ranges <- intersectMC(
             unlisted, cov_gr, ignore.strand = ignore.strand,
             simplify = simplify, ...
         )
+
     }
     if (method == "union") {
         ## For now, remove all mcols, however reduceMC may be useful if
         ## wishing to retain these for use with plotOverlaps()
         red_ranges <- reduceMC(
-            unlisted, ignore.strand = ignore.strand, simplify = simplify, ...
+            unlisted, ignore.strand = ignore.strand, simplify = simplify,
+            min.gapwidth = merge_within, ...
         )
     }
     ## Return the columns for overlaps
     ol <- lapply(x, function(x) overlapsAny(red_ranges, x))
     ol <- as.data.frame(ol)
+
     ## Ensure names are strictly retained
     names(ol) <- names(x)
     ol$n <- rowSums(ol)

R/plotOverlaps.R

@@ -30,7 +30,8 @@
 #' `draw.single/triple.venn`) for Venn Diagrams, and to
 #' \link[ComplexUpset]{upset} for UpSet plots
 #' @param .sort_sets passed to `sort_sets` in \link[ComplexUpset]{upset}
-#' @param min.gapwidth,ignore.strand Passed to \link[GenomicRanges]{reduce}
+#' @param ignore.strand Passed to \link[GenomicRanges]{reduce}
+#' @param merge_within Passed to \link{makeConsensus}
 #' @param sz_sets Text size for set size labels. Passed internally to
 #' `geom_text(size = sz_sets)`
 #' @param hj_sets Horizontal adjustment of set size labels
@@ -72,7 +73,7 @@ setMethod(
     x, type = c("auto", "venn", "upset"), var = NULL,
     f = c("mean", "median", "max", "min", "sd"),
     set_col = NULL, ..., .sort_sets = "ascending", hj_sets = 1.15,
-    sz_sets = 3.5, exp_sets = 0.25, min.gapwidth = 1L, ignore.strand = TRUE
+    sz_sets = 3.5, exp_sets = 0.25, merge_within = 1L, ignore.strand = TRUE
   ) {
 
     stopifnot(is(x, "GRangesList"))
@@ -87,8 +88,7 @@ setMethod(
 
     # Collapse as required
     gr <- makeConsensus(
-      x, var = var,
-      min.gapwidth = min.gapwidth, ignore.strand = ignore.strand
+      x, var = var, merge_within = merge_within, ignore.strand = ignore.strand
     )
 
     if (is.null(var) | type == "venn") {

R/setoptsMC.R

@@ -131,7 +131,7 @@ setMethod(
     col_names <- colnames(DF)
     if (n > 0) {
         DF2 <- list()
-        for (i in seq_along(col_names)){
+        for (i in seq_along(col_names)) {
             vec <- DF[[i]]
             nm <- col_names[[i]]
             type <- is(vec)[[1]]