importFrom clue,solve_LSAP

RGLab · Jul 18, 2023 · a2783c2 · a2783c2
1 parent 5b5dfe2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,11 +17,11 @@ Encoding: UTF-8
 Depends: R (>= 3.0.2)
 Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), 
    Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor,
-    mnormt
+    mnormt, clue
 Enhances: RBGL,graph
 License: Artistic-2.0
 Lazyload: yes
 URL: http://www.github.com/RGLab/flowStats
 BugReports: http://www.github.com/RGLab/flowStats/issues
 biocViews: ImmunoOncology, FlowCytometry, CellBasedAssays
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,6 +12,7 @@ importMethodsFrom(BiocGenerics, cbind, colnames, lapply, mapply, order,
                   table, unique)
 importFrom(corpcor,cov.shrink)
 
+importFrom(clue,solve_LSAP)
 importFrom(grDevices,cm.colors)
 importFrom(grDevices,gray)
 importFrom(grDevices,heat.colors)

diff --git a/R/spillover.R b/R/spillover.R
@@ -64,6 +64,7 @@
 #' of the New York Academy of Sciences, 677:167-184.
 #' @keywords methods
 #' @export
+#' @importFrom clue solve_LSAP
 setMethod("spillover",
           signature = signature(x = "flowSet"),
           definition = function(x, unstained = NULL, fsc = "FSC-A",
@@ -203,7 +204,7 @@ setMethod("spillover",
                 dists = sapply(colnames(inten),function(x)adist(x,rownames(inten)))
                 colnames(dists)=colnames(inten)
                 rownames(dists)=rownames(inten)                
-                solution=clue::solve_LSAP(t(dists))
+                solution=solve_LSAP(t(dists))
                 channel_order <- as.vector(solution)
                 for(i in 1:ncol(dists)){
                     cat("matching ",colnames(dists)[i]," to ", rownames(dists)[channel_order[i]],"\n")