Copy .weightedFDR() from csaw to avoid use of ":::"

Author: gksmyth

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: diffHic
-Version: 1.37.2
+Version: 1.37.3
 Date: 2024-05-11
 Title: Differential Analysis of Hi-C Data
 Author: Aaron Lun, Gordon Smyth

R/diClusters.R

@@ -5,7 +5,8 @@ diClusters <- function(data.list, result.list, target, equiweight=TRUE, cluster.
 #
 # written by Aaron Lun
 # created 12 January 2016
-# last modified 13 January 2016
+# last modified by Aaron Lun 4 June 2019
+# last modified 11 May 2024 to call local .weightedFDR
 {
     # Setting initial parameters.    
     if (missing(target)) {
@@ -49,7 +50,7 @@ diClusters <- function(data.list, result.list, target, equiweight=TRUE, cluster.
         last <- last + nrow(result.list[[x]])
     }
     all.ps <- unlist(all.ps)
-    adjp <- csaw:::.weightedFDR(all.ps, weights)
+    adjp <- .weightedFDR(all.ps, weights)
 
     # Getting the sign.
     if (is.na(fc.col)) { 

R/weightedFDR.R

@@ -0,0 +1,11 @@
+# Copied from csaw package
+
+.weightedFDR <- function(p, w) {
+    if (length(p)!=length(w)) { stop("weights and p-value vector are not of same length") }
+    o <- order(p)
+    p <- p[o]
+    w <- w[o]
+    adjp <- numeric(length(o))
+    adjp[o] <- rev(cummin(rev(sum(w)*p/cumsum(w))))
+    pmin(adjp, 1)
+}