@@ -1,12 +1,12 @@

 Package: SplicingGraphs

 Title: Tools for creating splicing graphs from annotations and RNA-Seq data

-Version: 0.8.3

+Version: 0.8.4

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

 License: Artistic-2.0

-Description: This package provides tools for creating splicing graphs based on

-	transcript annotations and additionally tools for testing for

-	differential splicing event usage based on genomic count data from

-	RNA-seq experiments. 

+Description: This package allows the user to create and manipulate splicing

+	graphs based on annotations that describe a gene model for a given

+	organism. Additionally the package allows the user to assign RNA-seq

+	reads to splicing graphs, and to count them.

 Maintainer: H. Pages <[email protected]>

 Depends: BiocGenerics, IRanges (>= 1.17.43), GenomicRanges,

 	 Rgraphviz (>= 2.3.7), GenomicFeatures (>= 1.11.8), Rsamtools

@@ -36,14 +36,14 @@ EX_OR_IN_LEVELS <- EX_OR_IN_LEVELS2[-4L]

 }

 .get_index_of_mcols_to_remove <- function(colnames,

-                                          keep.exon.mcols, keep.hits.mcols)

+                                          with.exon.mcols, with.hits.mcols)

 {

     ans <- integer(0)

-    if (!keep.exon.mcols) {

+    if (!with.exon.mcols) {

         idx <- match(EXON_MCOLS, colnames)

         ans <- c(ans, idx)

     }

-    if (!keep.hits.mcols) {

+    if (!with.hits.mcols) {

         idx <- grep("hits$", colnames)

         ans <- c(ans, idx)

     }

@@ -69,17 +69,17 @@ setMethod("intronsByTranscript", "SplicingGraphs", function(x) x@in_by_tx)

 ###

 setGeneric("sgedgesByTranscript", signature="x",

-    function(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+    function(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

         standardGeneric("sgedgesByTranscript")

 )

 setMethod("sgedgesByTranscript", "SplicingGraphs",

-    function(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+    function(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

     {

-        if (!isTRUEorFALSE(keep.exon.mcols))

-            stop("'keep.exon.mcols' must be TRUE or FALSE")

-        if (!isTRUEorFALSE(keep.hits.mcols))

-            stop("'keep.hits.mcols' must be TRUE or FALSE")

+        if (!isTRUEorFALSE(with.exon.mcols))

+            stop("'with.exon.mcols' must be TRUE or FALSE")

+        if (!isTRUEorFALSE(with.hits.mcols))

+            stop("'with.hits.mcols' must be TRUE or FALSE")

         ex_by_tx <- unlist(x)

         ex_partitioning <- PartitioningByEnd(ex_by_tx)

@@ -195,7 +195,7 @@ setMethod("sgedgesByTranscript", "SplicingGraphs",

         ## Drop unwanted columns.

         mcol_idx <- .get_index_of_mcols_to_remove(

                         colnames(ans_unlistData_mcols),

-                        keep.exon.mcols, keep.hits.mcols)

+                        with.exon.mcols, with.hits.mcols)

         if (length(mcol_idx) != 0L)

             ans_unlistData_mcols <- ans_unlistData_mcols[ , -mcol_idx,

                                                          drop=FALSE]

@@ -238,15 +238,15 @@ setMethod("sgedgesByTranscript", "SplicingGraphs",

 }

 setGeneric("sgedgesByGene", signature="x",

-    function(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+    function(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

         standardGeneric("sgedgesByGene")

 )

 setMethod("sgedgesByGene", "SplicingGraphs",

-    function(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+    function(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

     {

-        edges_by_tx <- sgedgesByTranscript(x, keep.exon.mcols=keep.exon.mcols,

-                                              keep.hits.mcols=keep.hits.mcols)

+        edges_by_tx <- sgedgesByTranscript(x, with.exon.mcols=with.exon.mcols,

+                                              with.hits.mcols=with.hits.mcols)

         edges0 <- unlist(edges_by_tx)

         edges0_mcols <- mcols(edges0)

         edges0_mcolnames <- colnames(edges0_mcols)

@@ -36,22 +36,22 @@

 \usage{

 \S4method{intronsByTranscript}{SplicingGraphs}(x)

-sgedgesByTranscript(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+sgedgesByTranscript(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

-sgedgesByGene(x, keep.exon.mcols=FALSE, keep.hits.mcols=FALSE)

+sgedgesByGene(x, with.exon.mcols=FALSE, with.hits.mcols=FALSE)

 }

 \arguments{

   \item{x}{

     A \link{SplicingGraphs} object.

   }

-  \item{keep.exon.mcols}{

-    Whether to keep the \emph{exon metadata columns} in the returned

-    object or not. Those columns are named: \code{exon_id}, \code{exon_name},

-    \code{exon_rank}, \code{start_SSid}, and \code{end_SSid}. They are

-    set to \code{NA} for edges of type intron.

+  \item{with.exon.mcols}{

+    Whether to include or not the \emph{exon metadata columns} in the

+    returned object. Those columns are named: \code{exon_id},

+    \code{exon_name}, \code{exon_rank}, \code{start_SSid}, and

+    \code{end_SSid}. They are set to \code{NA} for edges of type intron.

   }

-  \item{keep.hits.mcols}{

+  \item{with.hits.mcols}{

     TODO

   }

 }

@@ -131,7 +131,7 @@ edges_by_tx[names(edges_by_tx) \%in\% "geneB"]

 ## belongs to transcripts B1 and B2.

 ## Keep the "exon metadata columns".

-sgedgesByTranscript(sg, keep.exon.mcols=TRUE)

+sgedgesByTranscript(sg, with.exon.mcols=TRUE)

 ## Note that those cols are set to NA for edges of type intron.

 ## ---------------------------------------------------------------------

@@ -143,5 +143,5 @@ edges_by_gene[["geneB"]]

 ## Note that the 2 inner elements in 'edges_by_tx' with global edge

 ## id "geneB:3,4" are now merged into a single inner element.

-sgedgesByGene(sg, keep.exon.mcols=TRUE)

+sgedgesByGene(sg, with.exon.mcols=TRUE)

 }