@@ -41,8 +41,7 @@ Suggests:

     beachmat,

     Matrix,

     HDF5Array,

-    doParallel,

-    testthat

+    doParallel

 Collate:

     utils.R

     hasGRanges.R

@@ -121,11 +121,19 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {

 # TODO: To benefit from error recovery requires that bpStopOnError(BPPARAM) is

 #       TRUE but the default is FALSE. How to help the user? Probably don't

 #       want to override the user-specified value.

-BSmooth <- function(BSseq, ns = 70, h = 1000, maxGap = 10^8,

+BSmooth <- function(BSseq,

+                    ns = 70,

+                    h = 1000,

+                    maxGap = 10^8,

+                    keep.se = FALSE,

+                    verbose = TRUE,

+                    BPREDO = list(),

+                    BPPARAM = bpparam(),

+                    BACKEND = getRealizationBackend(),

+                    ...,

                     parallelBy = c("sample", "chromosome"),

-                    mc.preschedule = FALSE, mc.cores = 1, keep.se = FALSE,

-                    verbose = TRUE, BPREDO = list(), BPPARAM = bpparam(),

-                    BACKEND = getRealizationBackend(), ...) {

+                    mc.preschedule = FALSE,

+                    mc.cores = 1) {

     # Argument checks-----------------------------------------------------------

     # Check if this is a re-do.

@@ -8,6 +8,7 @@

     set to \code{2 * maxGap + 1} instead of \code{maxGap}. This likely did not

     affect results for users who left the default value of \code{maxGap = 10^8}

     but may have affected results for small values of \code{maxGap}.

+    }

   }

 }

@@ -4,34 +4,41 @@

   BSmooth, smoothing bisulfite sequence data

 }

 \description{

-  This implements the BSmooth algorithm for estimating methylation levels from

-  bisulfite sequencing data.}

+  This implements the BSmooth algorithm for estimating methylation levels from bisulfite sequencing data.}

 \usage{

-BSmooth(BSseq, ns = 70, h = 1000, maxGap = 10^8,

-  parallelBy = c("sample", "chromosome"), mc.preschedule = FALSE,

-  mc.cores = 1, keep.se = FALSE, verbose = TRUE, BPREDO = list(),

-  BPPARAM = bpparam(), BACKEND = getRealizationBackend(), ...)

+BSmooth(BSseq,

+        ns = 70,

+        h = 1000,

+        maxGap = 10^8,

+        keep.se = FALSE,

+        verbose = TRUE,

+        BPREDO = list(),

+        BPPARAM = bpparam(),

+        BACKEND = getRealizationBackend(),

+        ...,

+        parallelBy = c("sample", "chromosome"),

+        mc.preschedule = FALSE,

+        mc.cores = 1)

 }

 \arguments{

   \item{BSseq}{An object of class \code{BSseq}.}

   \item{ns}{The minimum number of methylation loci in a smoothing window.}

   \item{h}{The minimum smoothing window, in bases.}

-  \item{maxGap}{The maximum gap between two methylation loci, before the

-    smoothing is broken across the gap. The default smoothes each

-    chromosome separately.}

-  \item{parallelBy}{\strong{Deprecated}. See section, 'Parallelization and

-    progress monitoring'.}

-  \item{mc.preschedule}{\strong{Deprecated}. See section, 'Parallelization and

-    progress monitoring'.}

-  \item{mc.cores}{\strong{Deprecated}. See section, 'Parallelization and

-    progress monitoring'.}

+  \item{maxGap}{The maximum gap between two methylation loci, before the smoothing is broken across the gap.

+  The default smoothes each chromosome separately.}

+  \item{parallelBy}{\strong{Deprecated}.

+    See section 'Parallelization and progress monitoring' for further details.}

+  \item{mc.preschedule}{\strong{Deprecated}.

+    See section 'Parallelization and progress monitoring' for further details.}

+  \item{mc.cores}{\strong{Deprecated}.

+    See section 'Parallelization and progress monitoring' for further details.}

   \item{keep.se}{Should the estimated standard errors from the smoothing

     algorithm be kept. This will make the return object roughly 30

     percent bigger and is currently not be used for anything in \pkg{bsseq}.}

-  \item{verbose}{\strong{Deprecated}. See section, 'Parallelization and progress

-    monitoring'.}

-  \item{BPREDO}{Typically not used. See section, 'Parallelization and progress

-    monitoring'.}

+  \item{verbose}{\strong{Deprecated}.

+    See section, 'Parallelization and progress monitoring' for further details.}

+  \item{BPREDO}{Typically not used.

+    See section, 'Parallelization and progress monitoring' for further details.}

   \item{BPPARAM}{An optional \linkS4class{BiocParallelParam} instance

     determining the parallel back-end to be used during evaluation. Currently

     supported are \linkS4class{SerialParam} (Unix, Mac, Windows),

@@ -42,10 +49,11 @@ BSmooth(BSseq, ns = 70, h = 1000, maxGap = 10^8,

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

   \item{BACKEND}{\code{NULL} or a single string specifying the name of the

     realization backend. When the backend is set to \code{NULL}, the

-    \code{coef} and \code{se.coef} assays are realized in memory as an ordinary

-    matrix.}

+    \code{coef} and \code{se.coef} assays are realized in memory as ordinary

+    matrices, otherwise these are realized with the given \code{BACKEND}.}

   \item{...}{Additional arguments passed to the \linkS4class{RealizationSink}

-    constructor. See section, 'Realization backends'.}

+    constructor.

+    See section 'Realization backends' for further details.}

 }

 \details{

   \code{ns} and \code{h} are passed to the \code{locfit} function. The

@@ -53,7 +61,8 @@ BSmooth(BSseq, ns = 70, h = 1000, maxGap = 10^8,

   and a width big enough to contain \code{ns} number of methylation

   loci.

 }

-\section{Realization backend}{

+

+\section{Realization backends}{

   The \code{BSmooth()} function creates a new assay to store the coefficients

   used to construct the smoothed methylation estimates ((\code{coef}). An

   additional assay is also created if \code{keep.se == TRUE} (\code{se.coef}).

@@ -91,11 +100,10 @@ BSmooth(BSseq, ns = 70, h = 1000, maxGap = 10^8,

   relevant \linkS4class{RealizationSink} constructor. For example, the

   \code{...} argument can be used to specify the path to the HDF5 file to be

   used by \code{BSmooth()}. Please see the examples at the bottom of the page.

-

 }

 \section{Parallelization and progress monitoring}{

-  \code{BSmooth} now uses the \pkg{BiocParallel} package to implement

+  \code{BSmooth()} now uses the \pkg{BiocParallel} package to implement

   parallelization. This brings some notable improvements:

   \itemize{