@@ -1,5 +1,6 @@

 Package: SplicingGraphs

-Title: Creation, manipulation, visualization of splicing graphs

+Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

+	to them

 Version: 1.1.8

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages

 License: Artistic-2.0

@@ -207,22 +207,22 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

   Other topics related to this man page and documented in other packages:

   \itemize{

     \item The \code{\link[GenomicFeatures]{exonsBy}} and

-          \code{\link[GenomicFeatures]{transcriptsBy}} functions, and the

-          \link[GenomicFeatures]{TranscriptDb} class in the GenomicFeatures

-          package.

+          \code{\link[GenomicFeatures]{transcriptsBy}} functions, and

+          the \link[GenomicFeatures]{TranscriptDb} class in the

+          \pkg{GenomicFeatures} package.

-    \item The \link[GenomicRanges]{GRangesList} class in the GenomicRanges

-          package.

+    \item The \link[GenomicRanges]{GRangesList} class in the

+          \pkg{GenomicRanges} package.

     \item The \link[IRanges]{IntegerList}, \link[IRanges]{CharacterList},

-          and \link[IRanges]{DataFrame} classes in the IRanges package.

+          and \link[IRanges]{DataFrame} classes in the \pkg{IRanges} package.

   }

 }

@@ -4,12 +4,13 @@

 \alias{SplicingGraphs-package}

 \title{

-  Creation, manipulation, visualization of splicing graphs

+  Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

+  to them

 }

 \description{

-  The SplicingGraphs package allows the user to create, manipulate, and

-  visualize splicing graphs and their bubbles based on a gene model for

+  The \pkg{SplicingGraphs} package allows the user to create, manipulate,

+  and visualize splicing graphs and their bubbles based on a gene model for

   a given organism. Additionally it allows the user to assign RNA-seq

   reads to the edges of a set of splicing graphs, and to summarize them.

 }

@@ -19,12 +20,14 @@

 }

 \author{

-  SplicingGraphs is a reincarnation of an internal project, the SpliceGraph

-  package, originally written by D. Bindreither, M. Carlson, and M. Morgan.

-  The SpliceGraph package was never released as part of Bioconductor.

+  \pkg{SplicingGraphs} is a reincarnation of an internal project, the

+  \pkg{SpliceGraph} package, originally written by D. Bindreither,

+  M. Carlson, and M. Morgan.

+  The \pkg{SpliceGraph} package was never released as part of Bioconductor.

-  The SplicingGraphs package is a complete revamp (design and implementation)

-  of the SpliceGraph package, and was written by H. Pages.

+  The \pkg{SplicingGraphs} package is a complete revamp (design and

+  implementation) of the \pkg{SpliceGraph} package, and was written by

+  H. Pages.

   Maintainer: H. Pages <[email protected]>

 }

@@ -46,7 +49,7 @@

 }

 \seealso{

-  The man pages in the SplicingGraphs package are:

+  The man pages in the \pkg{SplicingGraphs} package are:

   \enumerate{

     \item The \link{SplicingGraphs} class.

@@ -65,8 +65,8 @@ removeReads(sg)

   If (a): you can find out whether reads in a BAM file are single- or

   paired-end with the \code{\link[Rsamtools]{quickCountBam}} utility

-  from the Rsamtools package. If they're paired-end, load them with

-  \code{\link[GenomicRanges]{readGAlignmentPairs}}

+  from the \pkg{Rsamtools} package. If they're paired-end, load them

+  with \code{\link[GenomicRanges]{readGAlignmentPairs}}

   instead of \code{\link[GenomicRanges]{readGAlignments}}, and that

   will pair them.

@@ -84,7 +84,7 @@ removeReads(sg)

                                   param=param0)

   }

   This will filter out records that have flag 0x100 (secondary alignment)

-  set to 1. See \code{?\link[Rsamtools]{scanBamFlag}} in the Rsamtools

+  set to 1. See \code{?\link[Rsamtools]{scanBamFlag}} in the \pkg{Rsamtools}

   package for more information.

   See the SAM Specs on the SAMtools project page at

   \url{http://samtools.sourceforge.net/} for a description of the

@@ -104,7 +104,7 @@ removeReads(sg)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

@@ -113,11 +113,11 @@ removeReads(sg)

     \item The \link[GenomicRanges]{GRangesList},

           \link[GenomicRanges]{GAlignments}, and

           \link[GenomicRanges]{GAlignmentPairs} classes

-          in the GenomicRanges package.

+          in the \pkg{GenomicRanges} package.

     \item The \code{\link[Rsamtools]{quickCountBam}} and

           \code{\link[Rsamtools]{ScanBamParam}} functions in the

-          Rsamtools package.

+          \pkg{Rsamtools} package.

   }

 }

@@ -44,7 +44,7 @@ ASCODE2DESC

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

@@ -151,7 +151,7 @@ reportReads(x, by=c("sgedge", "rsgedge", "tx", "gene"))

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

@@ -13,8 +13,8 @@

 }

 \description{

-  \code{plotTranscripts} uses the Gviz package to plot the exon structure

-  of a set of transcripts along genomic coordinates.

+  \code{plotTranscripts} uses the \pkg{Gviz} package to plot the exon

+  structure of a set of transcripts along genomic coordinates.

 }

 \usage{

@@ -47,22 +47,22 @@ plotTranscripts(x, reads=NULL, from=NA, to=NA)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

   Other topics related to this man page and documented in other packages:

   \itemize{

-    \item The \code{\link[Gviz]{plotTracks}} function in the Gviz package

-          that \code{plotTranscripts} is based on.

+    \item The \code{\link[Gviz]{plotTracks}} function in the \pkg{Gviz}

+          package that \code{plotTranscripts} is based on.

     \item The \link[GenomicRanges]{GRangesList},

           \link[GenomicRanges]{GAlignments}, and

           \link[GenomicRanges]{GAlignmentPairs} classes

-          in the GenomicRanges package.

+          in the \pkg{GenomicRanges} package.

-    \item The \link[GenomicFeatures]{TranscriptDb} class in the GenomicFeatures

-          package.

+    \item The \link[GenomicFeatures]{TranscriptDb} class in the

+          \pkg{GenomicFeatures} package.

   }

 }

@@ -90,7 +90,7 @@ uninformativeSSids(x)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

@@ -63,7 +63,7 @@ indeg(x)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

@@ -86,7 +86,7 @@ sgedgesByTranscript(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

@@ -68,7 +68,7 @@ slideshow(x)

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

 }

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

 \title{

   Little helpers for quick access to the toy data included in the

-  SplicingGraphs package

+  \pkg{SplicingGraphs} package

 }

 \description{

@@ -27,7 +27,7 @@ toy_overlaps()

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

@@ -36,11 +36,11 @@ toy_overlaps()

     \item The \link[GenomicRanges]{GRangesList},

           \link[GenomicRanges]{GAlignments}, and

           \link[GenomicRanges]{GAlignmentPairs} classes

-          in the GenomicRanges package.

+          in the \pkg{GenomicRanges} package.

     \item The \code{\link[GenomicFeatures]{makeTranscriptDbFromGFF}}

           function and the \link[GenomicFeatures]{TranscriptDb} class

-          in the GenomicFeatures package.

+          in the \pkg{GenomicFeatures} package.

   }

 }

@@ -60,7 +60,7 @@ txweight(x) <- value

 }

 \seealso{

-  This man page is part of the SplicingGraphs package.

+  This man page is part of the \pkg{SplicingGraphs} package.

   Please see \code{?`\link{SplicingGraphs-package}`} for an overview of the

   package and for an index of its man pages.

@@ -69,14 +69,14 @@ txweight(x) <- value

     \item The \link[GenomicRanges]{GRangesList},

           \link[GenomicRanges]{GAlignments}, and

           \link[GenomicRanges]{GAlignmentPairs} classes

-          in the GenomicRanges package.

+          in the \pkg{GenomicRanges} package.

     \item \link[GenomicRanges]{findOverlaps-methods} and

           \link[GenomicRanges]{encodeOverlaps-methods} in the

-          GenomicRanges package.

+          \pkg{GenomicRanges} package.

     \item The \code{\link[Rsamtools]{ScanBamParam}} function in the

-          Rsamtools package.

+          \pkg{Rsamtools} package.

   }

 }