... | ... |
@@ -35,8 +35,7 @@ importFrom(R.utils, "isGzipped", "gunzip") |
35 | 35 |
import(limma) |
36 | 36 |
importFrom(permute, "shuffleSet", "how") |
37 | 37 |
importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix") |
38 |
-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2", |
|
39 |
- "setRealizeBackend", "type") |
|
38 |
+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2") |
|
40 | 39 |
|
41 | 40 |
## |
42 | 41 |
## Exporting |
... | ... |
@@ -134,7 +134,7 @@ slots for representing smoothed data. This class is an extension of |
134 | 134 |
matrices (the latter two can only be combined if all objects have the |
135 | 135 |
same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using |
136 | 136 |
\link[base]{matrix} objects. See |
137 |
- \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}} for |
|
137 |
+ \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for |
|
138 | 138 |
alternative backends. |
139 | 139 |
} |
140 | 140 |
|
... | ... |
@@ -32,10 +32,10 @@ |
32 | 32 |
\code{mc.cores} to a value greater than 1 is not supported on MS |
33 | 33 |
Windows, see the help page for \code{mclapply}.} |
34 | 34 |
\item{verbose}{Make the function verbose.} |
35 |
- \item{BACKEND}{Which backend should be used for the 'M' and 'Cov' matrices? |
|
36 |
- The default, \code{NULL}, corresponds to using \link[base]{matrix} |
|
37 |
- objects. See \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}} |
|
38 |
- for alternative backends.} |
|
35 |
+ \item{BACKEND}{The backend used for the 'M' and 'Cov' matrices. The default, |
|
36 |
+ \code{NULL}, corresponds to using \link[base]{matrix} objects. See |
|
37 |
+ \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for |
|
38 |
+ alternative backends.} |
|
39 | 39 |
} |
40 | 40 |
\note{ |
41 | 41 |
Input files can either be gzipped or not. |
... | ... |
@@ -118,7 +118,7 @@ |
118 | 118 |
# An example constructing a HDF5Array-backed BSseq object |
119 | 119 |
# |
120 | 120 |
library(HDF5Array) |
121 |
- # See ?DelayedArray::setRealizeBackend for details |
|
121 |
+ # See ?DelayedArray::setRealizationBackend for details |
|
122 | 122 |
hdf5_bismarkBSseq <- read.bismark(files = infile, |
123 | 123 |
sampleNames = "test_data", |
124 | 124 |
rmZeroCov = FALSE, |