up

vignettes/miaViz.Rmd

@@ -63,7 +63,7 @@ However, if the `rank` is set not `NULL` a bar plot is returned. At the same
 time the `features` argument can be set to `NULL` (default).
 
 ```{r}
-GlobalPatterns <- transformCounts(GlobalPatterns, method = "relabundance")
+GlobalPatterns <- transformAssay(GlobalPatterns, method = "relabundance")
 ```
 
 ```{r}
@@ -261,7 +261,7 @@ plotColGraph(altExp(GlobalPatterns,"Genus"),
 library("miaTime")
 data(SilvermanAGutData, package="miaTime")
 tse <- SilvermanAGutData
-tse <- transformCounts(tse, method = "relabundance")
+tse <- transformAssay(tse, method = "relabundance")
 taxa <- getTopTaxa(tse, 2)
 ```
 
@@ -345,7 +345,7 @@ Principal Coordinates Analysis using Bray-Curtis dissimilarity on the
 library(miaTime)
 data(hitchip1006, package = "miaTime")
 tse <- hitchip1006
-tse <- transformCounts(tse, method = "relabundance")
+tse <- transformAssay(tse, method = "relabundance")
 ## Ordination with PCoA with Bray-Curtis dissimilarity
 tse <- runMDS(tse, FUN = vegan::vegdist, method = "bray", name = "PCoA_BC",
               assay.type = "relabundance", na.rm = TRUE)