@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 1.17.5

+Version: 1.17.6

 Encoding: UTF-8

 Title: Analyze, manage and store bisulfite sequencing data

 Description: A collection of tools for analyzing and visualizing bisulfite

@@ -83,7 +83,7 @@ BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,

     }

     # Process 'trans' and 'parameters'.

     if (is.null(trans)) {

-        trans <- function(x) NULL

+        trans <- function() NULL

     }

     if (is.null(parameters)) {

         parameters <- list()

@@ -152,7 +152,7 @@ combineList <- function(x, ..., BACKEND = NULL) {

         combine_smooths <- FALSE

         ans_coef <- NULL

         ans_se.coef <- NULL

-        ans_trans <- function(x) NULL

+        ans_trans <- function() NULL

         ans_parameters <- list()

     }

new file mode 100644

@@ -0,0 +1,27 @@

+context("GitHub issues")

+

+test_that("Issue 74 is fixed", {

+

+    # Can combine two BSseq objects with same loci but different names.

+    # (https://github.com/hansenlab/bsseq/issues/74#issue-341014110)

+    nloci <- 68164

+    nsamples <- 12

+    M <- matrix(rpois(nloci * nsamples, 10), ncol = nsamples)

+    Cov <- M + rpois(nloci * nsamples, 2)

+    gr <- sort(GRanges(

+        seqnames = sample(1:10, nloci, replace = TRUE),

+        ranges = IRanges(sample(1:10^7, nloci, replace = FALSE), width = 1)))

+    BS <- BSseq(M = M, Cov = Cov, gr = gr, sampleNames = paste0("V", 1:nsamples))

+    BS.avg <- collapseBSseq(BS, group = paste0("W", c(rep(1, 5), 2:8)))

+    BS.all <- combine(BS, BS.avg)

+    colnames(BS.all)

+

+    # As above, but when one of the BSseq objects contains additional colData.

+    # https://github.com/hansenlab/bsseq/issues/74#issue-341014110

+    BS2 <- BS

+    BS2$rep <- paste0("A", c(rep(1, 5), 2:8))

+    BS2.avg <- collapseBSseq(BS, group = paste0("W", c(rep(1, 5), 2:8)))

+    BS2.all <- combine(BS2,BS2.avg)

+    colnames(BS2.all)

+    colData(BS2.all)

+})