@@ -149,6 +149,7 @@ importFrom(tibble,tibble)

 importFrom(tidyr,unnest)

 importFrom(utils,installed.packages)

 importFrom(utils,packageVersion)

+importFrom(utils,read.delim)

 importFrom(utils,read.table)

 importFrom(withr,defer)

 useDynLib(NanoMethViz)

@@ -1,6 +1,6 @@

 #' Create BSSeq object from methylation tabix file

 #'

-#' @param methy the path to the methylation tabix file.

+#' @param methy the NanoMethResult object or path to the methylation tabix file.

 #' @param out_folder the folder to store intermediate files. One file is created

 #'   for each sample and contains columns "chr", "pos", "total" and

 #'   "methylated".

@@ -18,24 +18,27 @@ methy_to_bsseq <- function(

     verbose = TRUE

 ) {

     if (is(methy, "NanoMethResult")) {

-        methy <- NanoMethViz::methy(methy)

+        methy_path <- NanoMethViz::methy(methy)

+    } else {

+        methy_path <- methy

+        assert_that(fs::file_exists(methy_path))

     }

-    if (verbose) {

-        timed_log("creating intermediate files...")

-    }

+    timed_log("creating intermediate files...", verbose = verbose)

-    files <- convert_methy_to_dss(methy, out_folder)

+    files <- convert_methy_to_dss(methy_path, out_folder)

+

+    if (is(methy, "NanoMethResult")) {

+        sample_anno <- NanoMethViz::samples(methy)

+    } else {

+        sample_anno <- tibble::tibble(sample = files$sample)

+    }

     if (verbose) {

         timed_log("creating bsseq object...")

     }

-    out <- create_bsseq_from_files(

-        files$file_path,

-        files$sample,

-        verbose = verbose

-    )

+    out <- create_bsseq_from_files(files$file_path, sample_anno, verbose = verbose)

     if (verbose) {

         timed_log("done")

@@ -72,7 +75,7 @@ convert_methy_to_dss <- function(

 #' @importFrom purrr map

 #' @importFrom dplyr select distinct arrange mutate

 #' @importFrom bsseq BSseq

-create_bsseq_from_files <- function(paths, samples, verbose = TRUE) {

+create_bsseq_from_files <- function(paths, sample_anno, verbose = TRUE) {

     readr::local_edition(1) # temporary fix for vroom bad value

     read_dss <- purrr::partial(

         read_tsv,

@@ -84,6 +87,8 @@ create_bsseq_from_files <- function(paths, samples, verbose = TRUE) {

         )

     )

+    samples <- sample_anno$sample

+

     if (verbose) {

         timed_log("reading in parsed data...")

     }

@@ -145,9 +150,7 @@ create_bsseq_from_files <- function(paths, samples, verbose = TRUE) {

         sampleNames = samples

     )

-    SummarizedExperiment::colData(result) <- S4Vectors::DataFrame(

-        sample = samples

-    )

+    SummarizedExperiment::colData(result) <- S4Vectors::DataFrame(sample_anno)

     rownames(SummarizedExperiment::colData(result)) <- samples

@@ -94,9 +94,11 @@ assert_has_columns <- function(x, cols) {

     }

 }

-timed_log <- function(...) {

+timed_log <- function(..., verbose = TRUE) {

     time_stamp <- paste0("[", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "] ")

-    message(time_stamp, ...)

+    if (verbose) {

+        message(time_stamp, ...)

+    }

 }

 gene_pos_range <- function(nmr, gene) {

@@ -1,11 +1,24 @@

 test_that("methy_to_bsseq works", {

     # setup

     nmr <- load_example_nanomethresult()

-    bss <- methy_to_bsseq(NanoMethViz::methy(nmr))

+    bss <- methy_to_bsseq(nmr)

     # test

+    expect_no_error(methy_to_bsseq(methy(nmr)))

     expect_true(is(methy_to_bsseq(nmr), "BSseq"))

     expect_equal(ncol(bss), 6)

+    expect_equal(

+        nrow(SummarizedExperiment::colData(bss)),

+        nrow(NanoMethViz::samples(nmr))

+    )

+    expect_equal(

+        ncol(SummarizedExperiment::colData(bss)),

+        ncol(NanoMethViz::samples(nmr))

+    )

+    expect_equal(

+        colnames(SummarizedExperiment::colData(bss)),

+        colnames(NanoMethViz::samples(nmr))

+    )

 })

 test_that("bsseq_to_* works", {