Merge pull request #41 from suzannejin/master

changed pcor.bshrink so that the alr columns are 0 instead of NaN, otherwise the updateCutoff() function will give NaNs
tpq · Dec 15, 2023 · 32ef3a1 · 32ef3a1
2 parents ee4a796 + c693a82
commit 32ef3a1
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diff --git a/R/1-propr.R b/R/1-propr.R
@@ -149,6 +149,9 @@ propr <- function(counts,
   result@pairs <- vector("numeric")
   result@permutes <- list(NULL)
 
+  # ivar should not be NA, otherwise updateCutoffs does not work
+  if (metric == 'pcor.bshrink') result@ivar <- ivar_pcor
+
   # Clean row and column names
   result@matrix <- mat
   colnames(result@matrix) <- colnames(result@logratio)

diff --git a/R/1a-propr-backend.R b/R/1a-propr-backend.R
@@ -251,8 +251,8 @@ basis_shrinkage <- function(M, outtype = c("clr", "alr")) {
 
   # make output to have same dimensions as input
   if (outtype == "alr") {
-    PC <- cbind(PC, replicate(nrow(PC), NA))
-    PC <- rbind(PC, replicate(ncol(PC), NA))
+    PC <- cbind(PC, replicate(nrow(PC), 0))
+    PC <- rbind(PC, replicate(ncol(PC), 0))
     PC[nrow(PC), ncol(PC)] <- 1
   }