Binary files a/data/BS.chr22.rda and b/data/BS.chr22.rda differ

@@ -45,7 +45,7 @@ read.lister <- function(file) {

         Cov = as.matrix(tmp$Cov, ncol = 1),

         sampleNames = "reverse")

     BS <- combine(BS.forward, BS.reverse)

-    BS <- collapseBSseq(BS, columns = c("a", "a"))

+    BS <- collapseBSseq(BS, group = c("a", "a"), type = "integer")

     BS

 }

@@ -59,12 +59,5 @@ pData(BS.chr22)$Rep <- c("replicate1", "replicate2")

 validObject(BS.chr22)

 pData(BS.chr22)

-# NOTE: To reduce size of object, set the storage.mode() of assays to integer.

-#       (at this point they use doubles because collapseBSseq() returns

-#       doubles).

-storage.mode(assay(BS.chr22, 1)) <- "integer"

-storage.mode(assay(BS.chr22, 2)) <- "integer"

-

 save(BS.chr22, file = "BS.chr22.rda")

-library(tools)

-resaveRdaFiles("BS.chr22.rda")

+tools::resaveRdaFiles("BS.chr22.rda")