@@ -35,14 +35,18 @@ BSmooth(BSseq,

     monitoring' and 'Realization backends' for further details.}

   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}

     The dimensions of the chunks to use for writing the data to

-    disk. By default, \code{\link[HDF5Array]{getHDF5DumpChunkDim}()} using the

-    dimensions of the returned \linkS4class{BSseq} object will be used. See

-    \code{?\link[HDF5Array]{getHDF5DumpChunkDim}} for more information.}

+    disk. By default,

+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}

+    using the dimensions of the returned \linkS4class{BSseq} object will be

+    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}

+    for more information.}

   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}

     The compression level to use for writing the data to disk. By

-    default, \code{\link[HDF5Array]{getHDF5DumpCompressionLevel}()} will be

-    used. See \code{?\link[HDF5Array]{getHDF5DumpCompressionLevel}} for more

-    information.}

+    default,

+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}

+    will be used. See

+    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}

+    for more information.}

   \item{verbose}{A \code{logical(1)} indicating whether progress messages

     should be printed (default \code{TRUE}).}

 }

@@ -64,7 +68,7 @@ BSmooth(BSseq,

   The choice of realization backend is controlled by the \code{BACKEND}

   argument, which defaults to the current value of

-  \code{DelayedArray::\link[DelayedArray]{getRealizationBackend}()}.

+  \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.

   \code{BSmooth} supports the following realization backends:

@@ -134,8 +134,8 @@ slots for representing smoothed data. This class is an extension of

       matrices (the latter two can only be combined if all objects have the

       same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using

       \link[base]{matrix} objects. See

-      \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for

-      alternative backends.

+      \code{?DelayedArray::\link[DelayedArray:RealizationSink]{setRealizationBackend}}

+      for alternative backends.

       }

     \item{\code{strandCollapse(BSseq, shift = TRUE)}}{

@@ -31,7 +31,7 @@ BSseq(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,

 \details{

   The 'M', 'Cov', 'coef', and 'se.coef' matrix-like objects will be coerced to

   \linkS4class{DelayedMatrix} objects; see

-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of

+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of

   supported matrix-like objects. We recommend using \link[base]{matrix} objects

   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk

   storage of data.

@@ -24,7 +24,7 @@

 \details{

   The matrix-like elements of the list in the 'stats' slot will be coerced to

   \linkS4class{DelayedMatrix} objects; see

-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of

+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of

   supported matrix-like objects. We recommend using \link[base]{matrix} objects

   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk

   storage of data.

@@ -24,7 +24,7 @@

 \details{

   The 'stats' matrix-like object will be coerced to a

   \linkS4class{DelayedMatrix} object; see

-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of

+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of

   supported matrix-like objects. We recommend using \link[base]{matrix} objects

   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk

   storage of data.

@@ -41,8 +41,12 @@ findLoci(pattern,

   }

 }

 \details{

-  This function provides a convenience wrapper for finding methylation loci in a genome, based on running \code{\link[Biostrings]{vmatchPattern}()}.

-  Users requiring finer-grained control should directly use the \code{\link[Biostrings]{vmatchPattern}()} function and coerce the result to a \linkS4class{GRanges} object.

+  This function provides a convenience wrapper for finding methylation loci in

+  a genome, based on running

+  \code{\link[Biostrings:matchPattern]{vmatchPattern}()}.

+  Users requiring finer-grained control should directly use the

+  \code{\link[Biostrings:matchPattern]{vmatchPattern}()} function and coerce

+  the result to a \linkS4class{GRanges} object.

 }

 \value{

   A \linkS4class{GRanges} object storing the found loci.

@@ -52,7 +56,7 @@ findLoci(pattern,

 }

 \seealso{

   \itemize{

-    \item \code{Biostrings::\link[Biostrings]{vmatchPattern}()}

+    \item \code{Biostrings::\link[Biostrings:matchPattern]{vmatchPattern}()}

     \item \code{?BSgenome::`\link[BSgenome]{BSgenome-utils}`}

     }

 }

@@ -20,7 +20,7 @@ fisherTests(BSseq, group1, group2, lookup = NULL,

   \item{returnLookup}{Should a \sQuote{lookup} object be returned, see

     details.}

   \item{mc.cores}{The number of cores used.  Note that setting

-    \code{mc.cores} to a value greater than 1 is not  supported on MS

+    \code{mc.cores} to a value greater than 1 is not supported on MS

     Windows, see the help page for \code{mclapply}.}

   \item{verbose}{Should the function be verbose.}

 }

@@ -52,7 +52,7 @@ fisherTests(BSseq, group1, group2, lookup = NULL,

 }

 \seealso{

   \link[stats]{fisher.test} for information about Fisher's test.

-  \link[parallel]{mclapply} for the \code{mc.cores} argument.

+  \code{\link{mclapply}} for the \code{mc.cores} argument.

 }

 \examples{

 M <- matrix(1:9, 3,3)

@@ -33,7 +33,7 @@

     If \code{loci = NULL}, then \code{read.bismark()} will perform a first pass over the Bismark file to identify candidate loci.

     If \code{loci} is a \linkS4class{GenomicRanges} instance, then these form the candidate loci.

     In either case, the candidate loci will be filtered if

-    \code{rmZeroCov = TRUE} and collapsed if \code{strandCollapse = TRUE} to form the final set of methylation loci that form the \code{\link[SummarizedExperiment]{rowRanges}} of the returned \linkS4class{BSseq} object.

+    \code{rmZeroCov = TRUE} and collapsed if \code{strandCollapse = TRUE} to form the final set of methylation loci that form the \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{rowRanges}} of the returned \linkS4class{BSseq} object.

     See section 'Efficient use of \code{read.bismark()}' for further details.}

   \item{colData}{An optional \linkS4class{DataFrame} describing the samples.

     Row names, if present, become the column names of the \linkS4class{BSseq}

@@ -70,14 +70,18 @@

     with a new one? The content of the existing directory will be lost!}

   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}

     The dimensions of the chunks to use for writing the data to

-    disk. By default, \code{\link[HDF5Array]{getHDF5DumpChunkDim}()} using the

-    dimensions of the returned \linkS4class{BSseq} object will be used. See

-    \code{?\link[HDF5Array]{getHDF5DumpChunkDim}} for more information.}

+    disk. By default,

+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}

+    using the dimensions of the returned \linkS4class{BSseq} object will be

+    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}

+    for more information.}

   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}

     The compression level to use for writing the data to disk. By

-    default, \code{\link[HDF5Array]{getHDF5DumpCompressionLevel}()} will be

-    used. See \code{?\link[HDF5Array]{getHDF5DumpCompressionLevel}} for more

-    information.}

+    default,

+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}

+    will be used. See

+    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}

+    for more information.}

   \item{nThread}{The number of threads used by \code{\link[data.table]{fread}}

     when reading the \code{files}. Be careful when combining a parallel backend

     specified with \code{BPPARAM} with \code{nThread} > 1 because each worker

@@ -88,7 +92,7 @@

 \section{File formats}{

   The format of each file is automatically detected using the internal function \code{bsseq:::.guessBismarkFileType()}.

-  Files ending in \code{.gz}, \code{.bz2}, \code{.xz}, or \code{.zip} will be automatically decompressed to \code{\link[base]{tempdir}()}.

+  Files ending in \code{.gz}, \code{.bz2}, \code{.xz}, or \code{.zip} will be automatically decompressed to \code{\link{tempdir}()}.

   \subsection{Supported file formats}{

     Bismark's 'genome wide cytosine report' (\url{https://github.com/FelixKrueger/Bismark/tree/master/Docs#the-genome-wide-cytosine-report-optional-is-tab-delimited-in-the-following-format-1-based-coords}) and 'coverage' (\url{https://github.com/FelixKrueger/Bismark/tree/master/Docs#the-coverage-output-looks-like-this-tab-delimited-1-based-genomic-coords}) formats are both supported.

     If setting \code{loci = NULL}, then we strongly recommend using the 'genome wide cytosine report' output format because this includes strand information for each locus.

@@ -174,7 +178,7 @@

 \section{Realization backends}{

   The \code{read.bismark()} function creates a \linkS4class{BSseq} object with two assays, \code{M} and \code{Cov}.

   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.

-  The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link[DelayedArray]{getRealizationBackend}()}.

+  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}()}.

   \code{read.bismark()} supports the following realization backends: