| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: bsseq |
| 2 |
-Version: 1.27.4 |
|
| 2 |
+Version: 1.27.5 |
|
| 3 | 3 |
Encoding: UTF-8 |
| 4 | 4 |
Title: Analyze, manage and store bisulfite sequencing data |
| 5 | 5 |
Description: A collection of tools for analyzing and visualizing bisulfite |
| ... | ... |
@@ -34,7 +34,7 @@ Imports: |
| 34 | 34 |
BSgenome, |
| 35 | 35 |
Biostrings, |
| 36 | 36 |
utils, |
| 37 |
- HDF5Array (>= 1.15.19), |
|
| 37 |
+ HDF5Array (>= 1.19.11), |
|
| 38 | 38 |
rhdf5 |
| 39 | 39 |
Suggests: |
| 40 | 40 |
testthat, |
| ... | ... |
@@ -326,7 +326,7 @@ BSmooth <- function(BSseq, |
| 326 | 326 |
# HDF5Array::saveHDF5SummarizedExperiment(). |
| 327 | 327 |
dir <- dirname(h5_path) |
| 328 | 328 |
x <- BSseq |
| 329 |
- x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays) |
|
| 329 |
+ x@assays <- HDF5Array::shorten_assay2h5_links(x@assays) |
|
| 330 | 330 |
saveRDS(x, file = file.path(dir, "se.rds")) |
| 331 | 331 |
} |
| 332 | 332 |
BSseq |
| ... | ... |
@@ -252,9 +252,9 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(), |
| 252 | 252 |
stop("'replace' must be TRUE or FALSE")
|
| 253 | 253 |
} |
| 254 | 254 |
if (!dir.exists(dir)) {
|
| 255 |
- HDF5Array:::.create_dir(dir) |
|
| 255 |
+ HDF5Array::create_dir(dir) |
|
| 256 | 256 |
} else {
|
| 257 |
- HDF5Array:::.replace_dir(dir, replace) |
|
| 257 |
+ HDF5Array::replace_dir(dir, replace) |
|
| 258 | 258 |
} |
| 259 | 259 |
h5_path <- file.path(dir, "assays.h5") |
| 260 | 260 |
} else if (identical(BACKEND, NULL)) {
|
| ... | ... |
@@ -310,7 +310,7 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(), |
| 310 | 310 |
# NOTE: Save BSseq object; mimicing |
| 311 | 311 |
# HDF5Array::saveHDF5SummarizedExperiment(). |
| 312 | 312 |
x <- bsseq |
| 313 |
- x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays) |
|
| 313 |
+ x@assays <- HDF5Array::shorten_assay2h5_links(x@assays) |
|
| 314 | 314 |
saveRDS(x, file = file.path(dir, "se.rds")) |
| 315 | 315 |
} |
| 316 | 316 |
bsseq |
| ... | ... |
@@ -87,9 +87,9 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(), |
| 87 | 87 |
stop("'replace' must be TRUE or FALSE")
|
| 88 | 88 |
} |
| 89 | 89 |
if (!dir.exists(dir)) {
|
| 90 |
- HDF5Array:::.create_dir(dir) |
|
| 90 |
+ HDF5Array::create_dir(dir) |
|
| 91 | 91 |
} else {
|
| 92 |
- HDF5Array:::.replace_dir(dir, replace) |
|
| 92 |
+ HDF5Array::replace_dir(dir, replace) |
|
| 93 | 93 |
} |
| 94 | 94 |
h5_path <- file.path(dir, "assays.h5") |
| 95 | 95 |
} else if (identical(BACKEND, NULL)) {
|
| ... | ... |
@@ -144,7 +144,7 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(), |
| 144 | 144 |
# NOTE: Save BSseq object; mimicing |
| 145 | 145 |
# HDF5Array::saveHDF5SummarizedExperiment(). |
| 146 | 146 |
x <- bsseq |
| 147 |
- x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays) |
|
| 147 |
+ x@assays <- HDF5Array::shorten_assay2h5_links(x@assays) |
|
| 148 | 148 |
saveRDS(x, file = file.path(dir, "se.rds")) |
| 149 | 149 |
} |
| 150 | 150 |
bsseq |
| ... | ... |
@@ -423,9 +423,9 @@ read.bismark <- function(files, |
| 423 | 423 |
stop("'replace' must be TRUE or FALSE")
|
| 424 | 424 |
} |
| 425 | 425 |
if (!dir.exists(dir)) {
|
| 426 |
- HDF5Array:::.create_dir(dir) |
|
| 426 |
+ HDF5Array::create_dir(dir) |
|
| 427 | 427 |
} else {
|
| 428 |
- HDF5Array:::.replace_dir(dir, replace) |
|
| 428 |
+ HDF5Array::replace_dir(dir, replace) |
|
| 429 | 429 |
} |
| 430 | 430 |
} |
| 431 | 431 |
# Set verbosity used by internal functions. |
| ... | ... |
@@ -537,7 +537,7 @@ read.bismark <- function(files, |
| 537 | 537 |
# NOTE: Save BSseq object; mimicing |
| 538 | 538 |
# HDF5Array::saveHDF5SummarizedExperiment(). |
| 539 | 539 |
x <- bsseq |
| 540 |
- x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays) |
|
| 540 |
+ x@assays <- HDF5Array::shorten_assay2h5_links(x@assays) |
|
| 541 | 541 |
saveRDS(x, file = file.path(dir, "se.rds")) |
| 542 | 542 |
} |
| 543 | 543 |
bsseq |
