1. NanoMethViz
  2. R
  3. bsseq_to_edger.R
Browse code

Ensure that all system.file calls must work

shians authored on 10/10/2024 04:13:55
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ d06902a
... ... 
@@ -8,7 +8,7 @@
8 8 
 #' @export
9 9 
 #'
10 10 
 #' @examples
11 
-#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
11 
+#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz", mustWork = FALSE)
12 12 
 #' bsseq <- methy_to_bsseq(methy)
13 13 
 #' edger_mat <- bsseq_to_edger(bsseq)
14 14 
 bsseq_to_edger <- function(bsseq, regions = NULL) {
Browse code

Added check for non-negative prior count

shians authored on 27/05/2024 07:45:09
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ b2791c4
... ... 
@@ -80,6 +80,8 @@ methy_to_edger <- function(methy, regions = NULL, out_folder = tempdir(), verbos
80 80 
 #' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)
81 81
82 82 
 bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, drop_na = TRUE) {
83 
+    assertthat::assert_that(prior_count >= 0)
84 
+
83 85 
     if (prior_count < 1) {
84 86 
         warning("prior_count of 1 or higher is recommended")
85 87 
     }
Browse code

Refactored bsseq_to_edger helper functions

shians authored on 21/05/2024 05:22:47
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 46392ff
... ... 
@@ -12,19 +12,19 @@
12 12 
 #' bsseq <- methy_to_bsseq(methy)
13 13 
 #' edger_mat <- bsseq_to_edger(bsseq)
14 14 
 bsseq_to_edger <- function(bsseq, regions = NULL) {
15 
-    edger_col_names <- .get_edger_col_names(bsseq)
15 
+    edger_col_names <- bsseq_to_edger.get_edger_col_names(bsseq)
16 16
17 17 
     if (!is.null(regions)) {
18 18 
         assertthat::assert_that(is(regions, "data.frame"))
19 19 
         regions <- GenomicRanges::GRanges(regions)
20 20 
         edger_row_names <- regions$gene_id
21 21 
     } else {
22 
-        edger_row_names <- .get_edger_row_names(bsseq)
22 
+        edger_row_names <- bsseq_to_edger.get_edger_row_names(bsseq)
23 23 
     }
24 24
25 25 
     # construct matrix
26 
-    methylated <- .get_me_mat(bsseq, regions)
27 
-    unmethylated <- .get_un_mat(bsseq, regions)
26 
+    methylated <- bsseq_to_edger.get_me_mat(bsseq, regions)
27 
+    unmethylated <- bsseq_to_edger.get_un_mat(bsseq, regions)
28 28
29 29 
     edger_mat <- matrix(
30 30 
         0,
... ... 
@@ -89,12 +89,12 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, dro
89 89 
         regions <- GenomicRanges::GRanges(regions)
90 90 
         row_names <- regions$gene_id
91 91 
     } else {
92 
-        row_names <- .get_edger_row_names(bsseq)
92 
+        row_names <- bsseq_to_edger.get_edger_row_names(bsseq)
93 93 
     }
94 94
95 95 
     col_names <- SummarizedExperiment::colData(bsseq)$sample
96 
-    methylated <- .get_me_mat(bsseq, regions)
97 
-    unmethylated <- .get_un_mat(bsseq, regions)
96 
+    methylated <- bsseq_to_edger.get_me_mat(bsseq, regions)
97 
+    unmethylated <- bsseq_to_edger.get_un_mat(bsseq, regions)
98 98
99 99 
     log_mat <- log2(methylated + prior_count) - log2(unmethylated + prior_count)
100 100
... ... 
@@ -108,7 +108,8 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, dro
108 108 
     log_mat
109 109 
 }
110 110
111 
-.get_me_mat <- function(bsseq, regions) {
111 
+# helper functions ----
112 
+bsseq_to_edger.get_me_mat <- function(bsseq, regions) {
112 113 
     if (!is.null(regions)) {
113 114 
         bsseq::getCoverage(bsseq, regions, type = "M", what = "perRegionTotal")
114 115 
     } else {
... ... 
@@ -116,17 +117,17 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, dro
116 117 
     }
117 118 
 }
118 119
119 
-.get_un_mat <- function(bsseq, regions) {
120 
+bsseq_to_edger.get_un_mat <- function(bsseq, regions) {
120 121 
     if (!is.null(regions)) {
121 122 
         cov <- bsseq::getCoverage(bsseq, regions, type = "Cov", what = "perRegionTotal")
122 123 
     } else {
123 124 
         cov <- bsseq::getCoverage(bsseq, type = "Cov")
124 125 
     }
125 
-    me_mat <- .get_me_mat(bsseq, regions)
126 
+    me_mat <- bsseq_to_edger.get_me_mat(bsseq, regions)
126 127 
     cov - me_mat
127 128 
 }
128 129
129 
-.get_edger_col_names <- function(bsseq) {
130 
+bsseq_to_edger.get_edger_col_names <- function(bsseq) {
130 131 
     samples <- SummarizedExperiment::colData(bsseq)$sample
131 132 
     me_names <- paste0(samples, "_Me")
132 133 
     un_names <- paste0(samples, "_Un")
... ... 
@@ -139,7 +140,7 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, dro
139 140 
     edger_col_names
140 141 
 }
141 142
142 
-.get_edger_row_names <- function(bsseq) {
143 
+bsseq_to_edger.get_edger_row_names <- function(bsseq) {
143 144 
     gr <- bsseq::getBSseq(bsseq, type = "gr")
144 145 
     seq <- as.character(SummarizedExperiment::seqnames(gr))
145 146 
     pos <- as.integer(SummarizedExperiment::start(gr))
Browse code

Linting

shians authored on 29/02/2024 05:18:23
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 19dc3f0
... ... 
@@ -28,14 +28,14 @@ bsseq_to_edger <- function(bsseq, regions = NULL) {
28 28
29 29 
     edger_mat <- matrix(
30 30 
         0,
31 
-        ncol = 2*ncol(methylated),
31 
+        ncol = 2 * ncol(methylated),
32 32 
         nrow = nrow(methylated),
33 33 
         dimnames = list(edger_row_names, edger_col_names)
34 34 
     )
35 35
36 36 
     for (i in 0:(ncol(methylated) - 1)) {
37 
-        edger_mat[, 2*i + 1] <- methylated[, i + 1]
38 
-        edger_mat[, 2*i + 2] <- unmethylated[, i + 1]
37 
+        edger_mat[, 2 * i + 1] <- methylated[, i + 1]
38 
+        edger_mat[, 2 * i + 2] <- unmethylated[, i + 1]
39 39 
     }
40 40
41 41 
     edger_mat
... ... 
@@ -132,8 +132,8 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, dro
132 132 
     un_names <- paste0(samples, "_Un")
133 133 
     edger_col_names <- character(2 * length(samples))
134 134 
     for (i in 0:(length(samples) - 1)) {
135 
-        edger_col_names[2*i + 1] <- me_names[i + 1]
136 
-        edger_col_names[2*i + 2] <- un_names[i + 1]
135 
+        edger_col_names[2 * i + 1] <- me_names[i + 1]
136 
+        edger_col_names[2 * i + 2] <- un_names[i + 1]
137 137 
     }
138 138
139 139 
     edger_col_names
Browse code

Updated log methylation ratio conversion to drop regions not found in data

shians authored on 12/10/2023 22:26:39
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 1c09055
... ... 
@@ -68,6 +68,7 @@ methy_to_edger <- function(methy, regions = NULL, out_folder = tempdir(), verbos
68 68 
 #' @param regions the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per
69 69 
 #'   site.
70 70 
 #' @param prior_count the prior count added to avoid taking log of 0.
71 
+#' @param drop_na whether to drop rows with all NA values.
71 72 
 #'
72 73 
 #' @return a matrix containing log-methylation-ratios.
73 74 
 #' @export
... ... 
@@ -78,7 +79,7 @@ methy_to_edger <- function(methy, regions = NULL, out_folder = tempdir(), verbos
78 79 
 #' regions <- exons_to_genes(NanoMethViz::exons(nmr))
79 80 
 #' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)
80 81
81 
-bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2) {
82 
+bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2, drop_na = TRUE) {
82 83 
     if (prior_count < 1) {
83 84 
         warning("prior_count of 1 or higher is recommended")
84 85 
     }
... ... 
@@ -99,6 +100,11 @@ bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2) {
99 100
100 101 
     dimnames(log_mat) <- list(row_names, col_names)
101 102
103 
+    if (drop_na) {
104 
+        # drop rows that are all NA
105 
+        log_mat <- log_mat[!apply(is.na(log_mat), 1, all), ]
106 
+    }
107 
+
102 108 
     log_mat
103 109 
 }
104 110
Browse code

Fixed `bsseq_to_edger()` when using regions

Shians authored on 01/03/2022 04:49:26
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ b80dd9c
... ... 
@@ -13,7 +13,14 @@
13 13 
 #' edger_mat <- bsseq_to_edger(bsseq)
14 14 
 bsseq_to_edger <- function(bsseq, regions = NULL) {
15 15 
     edger_col_names <- .get_edger_col_names(bsseq)
16 
-    edger_row_names <- .get_edger_row_names(bsseq)
16 
+
17 
+    if (!is.null(regions)) {
18 
+        assertthat::assert_that(is(regions, "data.frame"))
19 
+        regions <- GenomicRanges::GRanges(regions)
20 
+        edger_row_names <- regions$gene_id
21 
+    } else {
22 
+        edger_row_names <- .get_edger_row_names(bsseq)
23 
+    }
17 24
18 25 
     # construct matrix
19 26 
     methylated <- .get_me_mat(bsseq, regions)
... ... 
@@ -34,6 +41,24 @@ bsseq_to_edger <- function(bsseq, regions = NULL) {
34 41 
     edger_mat
35 42 
 }
36 43
44 
+#' Convert NanoMethResult object to edgeR methylation matrix
45 
+#'
46 
+#' @inheritParams methy_to_bsseq
47 
+#' @param regions the regions to calculate log-methylation ratios over. If left
48 
+#' NULL, ratios will be calculated per site.
49 
+#'
50 
+#' @return a matrix compatible with the edgeR differential methylation pipeline
51 
+#' @export
52 
+#'
53 
+#' @examples
54 
+#' nmr <- load_example_nanomethresult()
55 
+#' edger_mat <- methy_to_edger(nmr)
56 
+#'
57 
+methy_to_edger <- function(methy, regions = NULL, out_folder = tempdir(), verbose = TRUE) {
58 
+    bsseq <- methy_to_bsseq(methy = methy, out_folder = out_folder, verbose = verbose)
59 
+    bsseq_to_edger(bsseq, regions = regions)
60 
+}
61 
+
37 62 
 #' Convert BSseq object to log-methylation-ratio matrix
38 63 
 #'
39 64 
 #' Creates a log-methylation-ratio matrix from a BSseq object that is useful for
Browse code

Added regions argument to bsseq_to_edger()

Shian Su authored on 26/07/2021 07:21:56
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 15fbf33
... ... 
@@ -1,6 +1,8 @@
1 1 
 #' Convert BSseq object to edgeR methylation matrix
2 2 
 #'
3 3 
 #' @param bsseq the BSseq object.
4 
+#' @param regions the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per
5 
+#'   site.
4 6 
 #'
5 7 
 #' @return a matrix compatible with the edgeR differential methylation pipeline
6 8 
 #' @export
... ... 
@@ -9,13 +11,13 @@
9 11 
 #' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
10 12 
 #' bsseq <- methy_to_bsseq(methy)
11 13 
 #' edger_mat <- bsseq_to_edger(bsseq)
12 
-bsseq_to_edger <- function(bsseq) {
14 
+bsseq_to_edger <- function(bsseq, regions = NULL) {
13 15 
     edger_col_names <- .get_edger_col_names(bsseq)
14 16 
     edger_row_names <- .get_edger_row_names(bsseq)
15 17
16 18 
     # construct matrix
17 
-    methylated <- .get_me_mat(bsseq)
18 
-    unmethylated <- .get_un_mat(bsseq)
19 
+    methylated <- .get_me_mat(bsseq, regions)
20 
+    unmethylated <- .get_un_mat(bsseq, regions)
19 21
20 22 
     edger_mat <- matrix(
21 23 
         0,
... ... 
@@ -38,7 +40,8 @@ bsseq_to_edger <- function(bsseq) {
38 40 
 #' dimensionality reduction plots.
39 41 
 #'
40 42 
 #' @param bsseq the BSseq object.
41 
-#' @param regions the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per site.
43 
+#' @param regions the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per
44 
+#'   site.
42 45 
 #' @param prior_count the prior count added to avoid taking log of 0.
43 46 
 #'
44 47 
 #' @return a matrix containing log-methylation-ratios.
... ... 
@@ -49,6 +52,7 @@ bsseq_to_edger <- function(bsseq) {
49 52 
 #' bsseq <- methy_to_bsseq(nmr)
50 53 
 #' regions <- exons_to_genes(NanoMethViz::exons(nmr))
51 54 
 #' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)
55 
+
52 56 
 bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2) {
53 57 
     if (prior_count < 1) {
54 58 
         warning("prior_count of 1 or higher is recommended")
Browse code

Updated examples to use NanoMethResult object for conversion examples

Shian Su authored on 26/07/2021 05:02:28
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ f848ac8
... ... 
@@ -38,24 +38,33 @@ bsseq_to_edger <- function(bsseq) {
38 38 
 #' dimensionality reduction plots.
39 39 
 #'
40 40 
 #' @param bsseq the BSseq object.
41 
+#' @param regions the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per site.
41 42 
 #' @param prior_count the prior count added to avoid taking log of 0.
42 43 
 #'
43 44 
 #' @return a matrix containing log-methylation-ratios.
44 45 
 #' @export
45 46 
 #'
46 47 
 #' @examples
47 
-#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
48 
-#' bsseq <- methy_to_bsseq(methy)
49 
-#' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq)
50 
-bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
48 
+#' nmr <- load_example_nanomethresult()
49 
+#' bsseq <- methy_to_bsseq(nmr)
50 
+#' regions <- exons_to_genes(NanoMethViz::exons(nmr))
51 
+#' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)
52 
+bsseq_to_log_methy_ratio <- function(bsseq, regions = NULL, prior_count = 2) {
51 53 
     if (prior_count < 1) {
52 54 
         warning("prior_count of 1 or higher is recommended")
53 55 
     }
54 56
57 
+    if (!is.null(regions)) {
58 
+        assertthat::assert_that(is(regions, "data.frame"))
59 
+        regions <- GenomicRanges::GRanges(regions)
60 
+        row_names <- regions$gene_id
61 
+    } else {
62 
+        row_names <- .get_edger_row_names(bsseq)
63 
+    }
64 
+
55 65 
     col_names <- SummarizedExperiment::colData(bsseq)$sample
56 
-    row_names <- .get_edger_row_names(bsseq)
57 
-    methylated <- .get_me_mat(bsseq)
58 
-    unmethylated <- .get_un_mat(bsseq)
66 
+    methylated <- .get_me_mat(bsseq, regions)
67 
+    unmethylated <- .get_un_mat(bsseq, regions)
59 68
60 69 
     log_mat <- log2(methylated + prior_count) - log2(unmethylated + prior_count)
61 70
... ... 
@@ -64,13 +73,21 @@ bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
64 73 
     log_mat
65 74 
 }
66 75
67 
-.get_me_mat <- function(bsseq) {
68 
-    bsseq::getBSseq(bsseq, type = "M")
76 
+.get_me_mat <- function(bsseq, regions) {
77 
+    if (!is.null(regions)) {
78 
+        bsseq::getCoverage(bsseq, regions, type = "M", what = "perRegionTotal")
79 
+    } else {
80 
+        bsseq::getCoverage(bsseq, type = "M")
81 
+    }
69 82 
 }
70 83
71 
-.get_un_mat <- function(bsseq) {
72 
-    cov <- bsseq::getBSseq(bsseq, type = "Cov")
73 
-    me_mat <- .get_me_mat(bsseq)
84 
+.get_un_mat <- function(bsseq, regions) {
85 
+    if (!is.null(regions)) {
86 
+        cov <- bsseq::getCoverage(bsseq, regions, type = "Cov", what = "perRegionTotal")
87 
+    } else {
88 
+        cov <- bsseq::getCoverage(bsseq, type = "Cov")
89 
+    }
90 
+    me_mat <- .get_me_mat(bsseq, regions)
74 91 
     cov - me_mat
75 92 
 }
76 93
Browse code

Removed trailing whitespace

shians authored on 11/09/2020 09:45:26
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 2b072e7
... ... 
@@ -46,7 +46,7 @@ bsseq_to_edger <- function(bsseq) {
46 46 
 #' @examples
47 47 
 #' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
48 48 
 #' bsseq <- methy_to_bsseq(methy)
49 
-#' log_m_ratio <- bsseq_to_methy_log_ratio(bsseq)
49 
+#' log_m_ratio <- bsseq_to_log_methy_ratio(bsseq)
50 50 
 bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
51 51 
     if (prior_count < 1) {
52 52 
         warning("prior_count of 1 or higher is recommended")
Browse code

Updated prior count recommendation

shians authored on 04/08/2020 00:46:36
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ d8a5ea1
... ... 
@@ -48,8 +48,8 @@ bsseq_to_edger <- function(bsseq) {
48 48 
 #' bsseq <- methy_to_bsseq(methy)
49 49 
 #' log_m_ratio <- bsseq_to_methy_log_ratio(bsseq)
50 50 
 bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
51 
-    if (prior_count <= 1) {
52 
-        warning("prior_count >1 is recommended")
51 
+    if (prior_count < 1) {
52 
+        warning("prior_count of 1 or higher is recommended")
53 53 
     }
54 54
55 55 
     col_names <- SummarizedExperiment::colData(bsseq)$sample
Browse code

Updated prior count recommendation

shians authored on 04/08/2020 00:46:21
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ b43e849
... ... 
@@ -49,7 +49,7 @@ bsseq_to_edger <- function(bsseq) {
49 49 
 #' log_m_ratio <- bsseq_to_methy_log_ratio(bsseq)
50 50 
 bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
51 51 
     if (prior_count <= 1) {
52 
-        warning("prior_count should be > 1 to avoid division by 0")
52 
+        warning("prior_count >1 is recommended")
53 53 
     }
54 54
55 55 
     col_names <- SummarizedExperiment::colData(bsseq)$sample
Browse code

Added warning for prior count <= 1

shians authored on 31/07/2020 12:32:12
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ e2baa48
... ... 
@@ -48,6 +48,10 @@ bsseq_to_edger <- function(bsseq) {
48 48 
 #' bsseq <- methy_to_bsseq(methy)
49 49 
 #' log_m_ratio <- bsseq_to_methy_log_ratio(bsseq)
50 50 
 bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
51 
+    if (prior_count <= 1) {
52 
+        warning("prior_count should be > 1 to avoid division by 0")
53 
+    }
54 
+
51 55 
     col_names <- SummarizedExperiment::colData(bsseq)$sample
52 56 
     row_names <- .get_edger_row_names(bsseq)
53 57 
     methylated <- .get_me_mat(bsseq)
Browse code

Updated file names

shians authored on 20/07/2020 01:49:21
Showing 1 changed files
R/bsseq_to_edger.R
History View file @ 324aa3f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,93 @@
1 
+#' Convert BSseq object to edgeR methylation matrix
2 
+#'
3 
+#' @param bsseq the BSseq object.
4 
+#'
5 
+#' @return a matrix compatible with the edgeR differential methylation pipeline
6 
+#' @export
7 
+#'
8 
+#' @examples
9 
+#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
10 
+#' bsseq <- methy_to_bsseq(methy)
11 
+#' edger_mat <- bsseq_to_edger(bsseq)
12 
+bsseq_to_edger <- function(bsseq) {
13 
+    edger_col_names <- .get_edger_col_names(bsseq)
14 
+    edger_row_names <- .get_edger_row_names(bsseq)
15 
+
16 
+    # construct matrix
17 
+    methylated <- .get_me_mat(bsseq)
18 
+    unmethylated <- .get_un_mat(bsseq)
19 
+
20 
+    edger_mat <- matrix(
21 
+        0,
22 
+        ncol = 2*ncol(methylated),
23 
+        nrow = nrow(methylated),
24 
+        dimnames = list(edger_row_names, edger_col_names)
25 
+    )
26 
+
27 
+    for (i in 0:(ncol(methylated) - 1)) {
28 
+        edger_mat[, 2*i + 1] <- methylated[, i + 1]
29 
+        edger_mat[, 2*i + 2] <- unmethylated[, i + 1]
30 
+    }
31 
+
32 
+    edger_mat
33 
+}
34 
+
35 
+#' Convert BSseq object to log-methylation-ratio matrix
36 
+#'
37 
+#' Creates a log-methylation-ratio matrix from a BSseq object that is useful for
38 
+#' dimensionality reduction plots.
39 
+#'
40 
+#' @param bsseq the BSseq object.
41 
+#' @param prior_count the prior count added to avoid taking log of 0.
42 
+#'
43 
+#' @return a matrix containing log-methylation-ratios.
44 
+#' @export
45 
+#'
46 
+#' @examples
47 
+#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
48 
+#' bsseq <- methy_to_bsseq(methy)
49 
+#' log_m_ratio <- bsseq_to_methy_log_ratio(bsseq)
50 
+bsseq_to_log_methy_ratio <- function(bsseq, prior_count = 2) {
51 
+    col_names <- SummarizedExperiment::colData(bsseq)$sample
52 
+    row_names <- .get_edger_row_names(bsseq)
53 
+    methylated <- .get_me_mat(bsseq)
54 
+    unmethylated <- .get_un_mat(bsseq)
55 
+
56 
+    log_mat <- log2(methylated + prior_count) - log2(unmethylated + prior_count)
57 
+
58 
+    dimnames(log_mat) <- list(row_names, col_names)
59 
+
60 
+    log_mat
61 
+}
62 
+
63 
+.get_me_mat <- function(bsseq) {
64 
+    bsseq::getBSseq(bsseq, type = "M")
65 
+}
66 
+
67 
+.get_un_mat <- function(bsseq) {
68 
+    cov <- bsseq::getBSseq(bsseq, type = "Cov")
69 
+    me_mat <- .get_me_mat(bsseq)
70 
+    cov - me_mat
71 
+}
72 
+
73 
+.get_edger_col_names <- function(bsseq) {
74 
+    samples <- SummarizedExperiment::colData(bsseq)$sample
75 
+    me_names <- paste0(samples, "_Me")
76 
+    un_names <- paste0(samples, "_Un")
77 
+    edger_col_names <- character(2 * length(samples))
78 
+    for (i in 0:(length(samples) - 1)) {
79 
+        edger_col_names[2*i + 1] <- me_names[i + 1]
80 
+        edger_col_names[2*i + 2] <- un_names[i + 1]
81 
+    }
82 
+
83 
+    edger_col_names
84 
+}
85 
+
86 
+.get_edger_row_names <- function(bsseq) {
87 
+    gr <- bsseq::getBSseq(bsseq, type = "gr")
88 
+    seq <- as.character(SummarizedExperiment::seqnames(gr))
89 
+    pos <- as.integer(SummarizedExperiment::start(gr))
90 
+    edger_row_names <- paste(seq, pos, sep = "-")
91 
+
92 
+    edger_row_names
93 
+}