Correctly fix method and add import

catavallejos · Mar 11, 2024 · 480bf74 · 480bf74
1 parent 845dc23
commit 480bf74
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/NAMESPACE b/NAMESPACE
@@ -145,6 +145,7 @@ importFrom(stats,lag)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
+importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,rgamma)
 importFrom(stats,rlnorm)

diff --git a/R/Methods.R b/R/Methods.R
@@ -137,6 +137,7 @@ setMethod(
 #'
 #' @author Catalina A. Vallejos \email{cnvallej@@uc.cl}
 #' @author Nils Eling \email{eling@@ebi.ac.uk}
+#' @importFrom stats na.omit
 #' @export
 setMethod("Summary",
           signature = "BASiCS_Chain",
@@ -156,7 +157,8 @@ setMethod("Summary",
         dimnames = list(colnames(n), c("median", "lower", "upper"))
       )
       HPD[, 1] <- colMedians(n, na.rm = na.rm)
-      HPD[, 2:3] <- apply(n, 2, function(col) {
+      ind_not_na <- !is.na(HPD[, 1])
+      HPD[ind_not_na, 2:3] <- apply(n[, ind_not_na, drop=FALSE], 2, function(col) {
         if (na.rm) {
           col <- na.omit(col)
           # avoid coda error for no samples