- According to Martin, this is the 'simplest solution', which lets the help system resolve the location dynamically (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016552.html)
Peter Hickey authored on 04/06/2020 03:06:19
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@@ -35,18 +35,13 @@ BSmooth(BSseq, |
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monitoring' and 'Realization backends' for further details.} |
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\item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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The dimensions of the chunks to use for writing the data to |
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- disk. By default, |
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- \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
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- using the dimensions of the returned \linkS4class{BSseq} object will be
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- used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
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- for more information.} |
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+ disk. By default, \code{\link{getHDF5DumpChunkDim}()} using the dimensions
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+ of the returned \linkS4class{BSseq} object will be used. See
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+ \code{?{getHDF5DumpChunkDim}} for more information.}
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| 43 | 41 |
\item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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The compression level to use for writing the data to disk. By |
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- default, |
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- \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
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- will be used. See |
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- \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
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- for more information.} |
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+ default, \code{\link{getHDF5DumpCompressionLevel}()} will be used. See
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+ \code{?\link{getHDF5DumpCompressionLevel}} for more information.}
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\item{verbose}{A \code{logical(1)} indicating whether progress messages
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should be printed (default \code{TRUE}).}
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} |
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@@ -67,8 +62,7 @@ BSmooth(BSseq, |
| 67 | 62 |
\linkS4class{HDF5Array}, for example.
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| 68 | 63 |
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The choice of realization backend is controlled by the \code{BACKEND}
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- argument, which defaults to the current value of |
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- \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.
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+ argument, which defaults to the current value of \code{DelayedArray::\link{getRealizationBackend}()}.
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| 72 | 66 |
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\code{BSmooth} supports the following realization backends:
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| 74 | 68 |
|
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@@ -134,9 +134,8 @@ slots for representing smoothed data. This class is an extension of |
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matrices (the latter two can only be combined if all objects have the |
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same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using
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\link[base]{matrix} objects. See
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- \code{?DelayedArray::\link[DelayedArray:RealizationSink]{setRealizationBackend}}
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- for alternative backends. |
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- } |
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+ \code{?DelayedArray::\link{setRealizationBackend}} for alternative
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+ backends.} |
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\item{\code{strandCollapse(BSseq, shift = TRUE)}}{
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|
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@@ -71,17 +71,14 @@ |
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\item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
|
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The dimensions of the chunks to use for writing the data to |
| 73 | 73 |
disk. By default, |
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- \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
|
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- using the dimensions of the returned \linkS4class{BSseq} object will be
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- used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
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- for more information.} |
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+ \code{\link{getHDF5DumpChunkDim}()} using the dimensions of the returned
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+ \linkS4class{BSseq} object will be used. See
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+ \code{?\link{getHDF5DumpChunkDim}} for more information.}
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\item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
|
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The compression level to use for writing the data to disk. By |
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default, |
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- \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
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- will be used. See |
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- \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
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- for more information.} |
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+ \code{\link{getHDF5DumpCompressionLevel}()} will be used. See
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+ \code{?\link{getHDF5DumpCompressionLevel}} for more information.}
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\item{nThread}{The number of threads used by \code{\link[data.table]{fread}}
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when reading the \code{files}. Be careful when combining a parallel backend
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specified with \code{BPPARAM} with \code{nThread} > 1 because each worker
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@@ -178,7 +175,7 @@ |
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\section{Realization backends}{
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The \code{read.bismark()} function creates a \linkS4class{BSseq} object with two assays, \code{M} and \code{Cov}.
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The choice of \emph{realization backend} controls whether these assays are stored in-memory as an ordinary \link[base]{matrix} or on-disk as a \linkS4class{HDF5Array}, for example.
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- The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.
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+ The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link{getRealizationBackend}()}.
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\code{read.bismark()} supports the following realization backends:
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