Browse code

Close issue #74

- Small tweak to default @trans function in BSseq() and combine().
- Add unit test

Peter Hickey authored on 15/10/2018 05:04:53
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 Package: bsseq
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-Version: 1.17.5
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+Version: 1.17.6
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 Encoding: UTF-8
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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@@ -83,7 +83,7 @@ BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,
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     }
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     # Process 'trans' and 'parameters'.
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     if (is.null(trans)) {
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-        trans <- function(x) NULL
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+        trans <- function() NULL
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     }
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     if (is.null(parameters)) {
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         parameters <- list()
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@@ -152,7 +152,7 @@ combineList <- function(x, ..., BACKEND = NULL) {
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         combine_smooths <- FALSE
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         ans_coef <- NULL
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         ans_se.coef <- NULL
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-        ans_trans <- function(x) NULL
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+        ans_trans <- function() NULL
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         ans_parameters <- list()
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     }
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new file mode 100644
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+context("GitHub issues")
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+
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+test_that("Issue 74 is fixed", {
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+
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+    # Can combine two BSseq objects with same loci but different names.
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+    # (https://github.com/hansenlab/bsseq/issues/74#issue-341014110)
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+    nloci <- 68164
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+    nsamples <- 12
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+    M <- matrix(rpois(nloci * nsamples, 10), ncol = nsamples)
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+    Cov <- M + rpois(nloci * nsamples, 2)
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+    gr <- sort(GRanges(
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+        seqnames = sample(1:10, nloci, replace = TRUE),
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+        ranges = IRanges(sample(1:10^7, nloci, replace = FALSE), width = 1)))
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+    BS <- BSseq(M = M, Cov = Cov, gr = gr, sampleNames = paste0("V", 1:nsamples))
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+    BS.avg <- collapseBSseq(BS, group = paste0("W", c(rep(1, 5), 2:8)))
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+    BS.all <- combine(BS, BS.avg)
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+    colnames(BS.all)
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+
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+    # As above, but when one of the BSseq objects contains additional colData.
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+    # https://github.com/hansenlab/bsseq/issues/74#issue-341014110
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+    BS2 <- BS
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+    BS2$rep <- paste0("A", c(rep(1, 5), 2:8))
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+    BS2.avg <- collapseBSseq(BS, group = paste0("W", c(rep(1, 5), 2:8)))
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+    BS2.all <- combine(BS2,BS2.avg)
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+    colnames(BS2.all)
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+    colData(BS2.all)
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+})