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

 Package: SplicingGraphs

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

-Version: 0.8.1

+Version: 0.8.2

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

 License: Artistic-2.0

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

@@ -21,6 +21,7 @@ Collate: utils.R

 	 igraph-utils.R

 	 SplicingGraphs-class.R

 	 sgedgesByTranscript-methods.R

+	 txpath-methods.R

 	 sgedges-methods.R

 	 sgraph-methods.R

 	 bubbles-methods.R

@@ -80,9 +80,11 @@ export(

     ## sgedgesByTranscript-methods.R:

     sgedgesByTranscript,

-    ## sgedges-methods.R:

-    txpaths,

+    ## txpath-methods.R:

+    txpath,

     UATXHcount,

+

+    ## sgedges-methods.R:

     sgedges,

     sgnodes,

     outdeg, indeg,

@@ -100,7 +102,7 @@ exportMethods(

     plotTranscripts,

     SplicingGraphs,

     sgedgesByTranscript,

-    txpaths,

+    txpath,

     UATXHcount,

     sgedges,

     sgnodes,

@@ -369,19 +369,19 @@ setMethod("plotTranscripts", "SplicingGraphs",

     if (!is.null(tx_id))

         gene_mcols$tx_id <- tx_id

-    ## Set "txpaths" metadata col.

-    if ("txpaths" %in% colnames(gene_mcols))

-        stop("'gene' already has metadata column txpaths")

+    ## Set "txpath" metadata col.

+    if ("txpath" %in% colnames(gene_mcols))

+        stop("'gene' already has metadata column txpath")

     if (on.minus.strand) {

-        txpaths <- rbind(SSids$end_SSid, SSids$start_SSid)

+        txpath <- rbind(SSids$end_SSid, SSids$start_SSid)

     } else {

-        txpaths <- rbind(SSids$start_SSid, SSids$end_SSid)

+        txpath <- rbind(SSids$start_SSid, SSids$end_SSid)

     }

-    txpaths_partitioning_end <- end(PartitioningByEnd(gene)) * 2L

-    txpaths_partitioning <- PartitioningByEnd(txpaths_partitioning_end)

-    names(txpaths_partitioning) <- tx_id

-    txpaths <- splitAsList(as.vector(txpaths), txpaths_partitioning)

-    gene_mcols$txpaths <- txpaths

+    txpath_partitioning_end <- end(PartitioningByEnd(gene)) * 2L

+    txpath_partitioning <- PartitioningByEnd(txpath_partitioning_end)

+    names(txpath_partitioning) <- tx_id

+    txpath <- splitAsList(as.vector(txpath), txpath_partitioning)

+    gene_mcols$txpath <- txpath

     mcols(gene) <- gene_mcols

     gene

@@ -236,15 +236,15 @@ setMethod("bubbles", "SplicingGraphs",

 setMethod("bubbles", "ANY",

     function(x)

     {

-        txpaths <- txpaths(x)

-        bubbles(txpaths)

+        txpath <- txpath(x)

+        bubbles(txpath)

     }

 )

 setMethod("bubbles", "IntegerList",

     function(x)

     {

-        txpathmat <- make_matrix_from_txpaths(x)

+        txpathmat <- make_matrix_from_txpath(x)

         #outdeg <- outdeg(x)

         #indeg <- indeg(x)

         #.extract_bubbles_from_txpathmat(txpathmat, outdeg, indeg)

@@ -3,12 +3,6 @@

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

-.get_sgnodes_from_txpaths <- function(txpaths)

-{

-    SSids <- unique(unlist(txpaths, use.names=FALSE))

-    c("R", sort(SSids), "L")

-}

-

 .get_sgnodes_from_sgedges <- function(sgedges)

 {

     from <- sgedges[ , "from"]

@@ -17,68 +11,6 @@

     c("R", sort(SSids), "L")

 }

-make_matrix_from_txpaths <- function(txpaths)

-{

-    sgnodes <- .get_sgnodes_from_txpaths(txpaths)

-    ans_nrow <- length(txpaths)

-    ans_ncol <- length(sgnodes)

-    ans_dimnames <- list(names(txpaths), sgnodes)

-    ans <- matrix(FALSE , nrow=ans_nrow, ncol=ans_ncol, dimnames=ans_dimnames)

-    ans[ , 1L] <- ans[ , ans_ncol] <- TRUE

-    i <- cbind(rep.int(seq_along(txpaths), elementLengths(txpaths)),

-               unlist(txpaths, use.names=FALSE) + 1L)

-    ans[i] <- TRUE

-    ans

-}

-

-

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

-### txpaths() accessor

-###

-### Gets the splicing paths.

-### Returns them in a named IntegerList with 1 top-level element per

-### transcript in the specified gene. Each top-level element 'txpaths[[i]]'

-### contains the splicing site ids for the i-th transcript.

-###

-

-setGeneric("txpaths", signature="x",

-    function(x, as.matrix=FALSE) standardGeneric("txpaths")

-)

-

-### Should return a CompressedIntegerList.

-setMethod("txpaths", "SplicingGraphs",

-    function(x, as.matrix=FALSE)

-    {

-        if (length(x) != 1L)

-            stop("'x' must be a SplicingGraphs object of length 1")

-        if (!isTRUEorFALSE(as.matrix))

-            stop("'as.matrix' must be TRUE or FALSE")

-        ans <- mcols(unlist(x, use.names=FALSE))[ , "txpaths"]

-        if (as.matrix)

-            ans <- make_matrix_from_txpaths(ans)

-        ans

-    }

-)

-

-

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

-### UATXHcount() accessor

-###

-

-setGeneric("UATXHcount", signature="x",

-    function(x) standardGeneric("UATXHcount")

-)

-

-### Should return an integer vector or a NULL.

-setMethod("UATXHcount", "SplicingGraphs",

-    function(x)

-    {

-        if (length(x) != 1L)

-            stop("'x' must be a SplicingGraphs object of length 1")

-        mcols(unlist(x, use.names=FALSE))[["UATXHcount"]]

-    }

-)

-

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

 ### sgedges() extractor

@@ -86,29 +18,29 @@ setMethod("UATXHcount", "SplicingGraphs",

 ### Returns the splicing graph in a DataFrame with 1 row per edge.

 ###

-### 'txpaths' must be an IntegerList containing all the splicing paths (1 per

-### transcript) for a given gene. Should have been obtained thru the txpaths()

+### 'txpath' must be an IntegerList containing all the splicing paths (1 per

+### transcript) for a given gene. Should have been obtained thru the txpath()

 ### accessor. Returns a 4-col (or 5-col if 'UATXHcount' is supplied) data.frame

 ### representing the splicing graph.

-.make_sgedges0_from_txpaths <- function(txpaths, UATXHcount=NULL)

+.make_sgedges0_from_txpath <- function(txpath, UATXHcount=NULL)

 {

     if (!is.null(UATXHcount)) {

         if (!is.integer(UATXHcount))

             stop("'UATXHcount' must be an integer vector or NULL")

-        if (length(UATXHcount) != length(txpaths))

+        if (length(UATXHcount) != length(txpath))

             stop("when not NULL, 'UATXHcount' must have ",

-                 "the same length as 'txpaths'")

+                 "the same length as 'txpath'")

     }

-    sgedges0s <- lapply(seq_along(txpaths),

+    sgedges0s <- lapply(seq_along(txpath),

                         function(i) {

-                            txpath <- txpaths[[i]]

-                            txpath_len <- length(txpath)

-                            if (txpath_len %% 2L != 0L)

-                                stop("some paths in 'txpaths' contain ",

+                            txpath_i <- txpath[[i]]

+                            txpath_i_len <- length(txpath_i)

+                            if (txpath_i_len %% 2L != 0L)

+                                stop("some paths in 'txpath' contain ",

                                      "an odd number of splicing site ids")

-                            from <- c("R", txpath)

-                            to <- c(txpath, "L")

-                            nexons <- txpath_len %/% 2L

+                            from <- c("R", txpath_i)

+                            to <- c(txpath_i, "L")

+                            nexons <- txpath_i_len %/% 2L

                             if (nexons == 0L) {

                                 ex_or_in <- EX_OR_IN_LEVELS[3L]

                             } else {

@@ -128,9 +60,9 @@ setMethod("UATXHcount", "SplicingGraphs",

                         })

     nedges_per_tx <- sapply(sgedges0s, nrow)

     sgedges0 <- do.call(rbind, sgedges0s)

-    tx_id <- names(txpaths)

+    tx_id <- names(txpath)

     if (is.null(tx_id))

-        tx_id <- seq_along(txpaths)

+        tx_id <- seq_along(txpath)

     tx_id <- rep.int(factor(tx_id, levels=tx_id), nedges_per_tx)

     sgedges0$tx_id <- tx_id

     if (!is.null(UATXHcount))

@@ -246,13 +178,13 @@ setMethod("sgedges", "SplicingGraphs",

     {

         if (!isTRUEorFALSE(keep.dup.edges))

             stop("'keep.dup.edges' must be TRUE or FALSE")

-        txpaths <- txpaths(x)

+        txpath <- txpath(x)

         if (is.null(UATXHcount))

             UATXHcount <- UATXHcount(x)

         if (keep.dup.edges)

-            return(sgedges(txpaths, UATXHcount=UATXHcount,

+            return(sgedges(txpath, UATXHcount=UATXHcount,

                                     keep.dup.edges=keep.dup.edges))

-        sgedges0 <- sgedges(txpaths, UATXHcount=UATXHcount,

+        sgedges0 <- sgedges(txpath, UATXHcount=UATXHcount,

                                      keep.dup.edges=TRUE)

         exon_hits <- .extract_sgedges_exon_hits(x)

         intron_hits <- .extract_sgedges_intron_hits(x)

@@ -269,7 +201,7 @@ setMethod("sgedges", "SplicingGraphs",

 setMethod("sgedges", "IntegerList",

     function(x, UATXHcount=NULL, keep.dup.edges=FALSE)

     {

-        sgedges0 <- .make_sgedges0_from_txpaths(x, UATXHcount=UATXHcount)

+        sgedges0 <- .make_sgedges0_from_txpath(x, UATXHcount=UATXHcount)

         sgedges(sgedges0, keep.dup.edges=keep.dup.edges)

     }

 )

@@ -300,13 +232,13 @@ setGeneric("sgnodes", signature="x",

 setMethod("sgnodes", "ANY",

     function(x)

     {

-        txpaths <- txpaths(x)

-        sgnodes(txpaths)

+        txpath <- txpath(x)

+        sgnodes(txpath)

     }

 )

 setMethod("sgnodes", "IntegerList",

-    function(x) .get_sgnodes_from_txpaths(x)

+    function(x) get_sgnodes_from_txpath(x)

 )

 setMethod("sgnodes", "data.frame",

new file mode 100644

@@ -0,0 +1,89 @@

+### =========================================================================

+### "txpath" (and related) methods

+### -------------------------------------------------------------------------

+

+

+get_sgnodes_from_txpath <- function(txpath)

+{

+    SSids <- unique(unlist(txpath, use.names=FALSE))

+    c("R", sort(SSids), "L")

+}

+

+make_matrix_from_txpath <- function(txpath)

+{

+    sgnodes <- get_sgnodes_from_txpath(txpath)

+    ans_nrow <- length(txpath)

+    ans_ncol <- length(sgnodes)

+    ans_dimnames <- list(names(txpath), sgnodes)

+    ans <- matrix(FALSE , nrow=ans_nrow, ncol=ans_ncol, dimnames=ans_dimnames)

+    ans[ , 1L] <- ans[ , ans_ncol] <- TRUE

+    i <- cbind(rep.int(seq_along(txpath), elementLengths(txpath)),

+               unlist(txpath, use.names=FALSE) + 1L)

+    ans[i] <- TRUE

+    ans

+}

+

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### txpath() accessor

+###

+### Gets the splicing paths.

+### Returns them in a named IntegerList object (actually a

+### CompressedIntegerList instance) with 1 list element per transcript.

+### Each list element 'txpath[[i]]' contains the Splicing Site ids for the

+### i-th transcript.

+###

+

+setGeneric("txpath", signature="x",

+    function(x, as.matrix=FALSE) standardGeneric("txpath")

+)

+

+setMethod("txpath", "GRangesList",

+    function(x, as.matrix=FALSE)

+    {

+        if (!identical(as.matrix, FALSE))

+            stop("the 'as.matrix' arg is not supported ",

+                 "when 'x' is a GRangesList object")

+        ans <- mcols(x)[ , "txpath"]

+        x_names <- names(x)

+        if (!is.null(x_names))

+            names(ans) <- x_names

+        ans

+    }

+)

+

+setMethod("txpath", "SplicingGraphs",

+    function(x, as.matrix=FALSE)

+    {

+        if (length(x) != 1L)

+            stop("'x' must be a SplicingGraphs object of length 1")

+        if (!isTRUEorFALSE(as.matrix))

+            stop("'as.matrix' must be TRUE or FALSE")

+        ## Same as 'x[[1]]' but should be faster.

+        x_1 <- unlist(x, use.names=FALSE)

+        ans <- txpath(x_1)

+        if (!as.matrix)

+            return(ans)

+        make_matrix_from_txpath(ans)

+    }

+)

+

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### UATXHcount() accessor

+###

+

+setGeneric("UATXHcount", signature="x",

+    function(x) standardGeneric("UATXHcount")

+)

+

+### Should return an integer vector or a NULL.

+setMethod("UATXHcount", "SplicingGraphs",

+    function(x)

+    {

+        if (length(x) != 1L)

+            stop("'x' must be a SplicingGraphs object of length 1")

+        mcols(unlist(x, use.names=FALSE))[["UATXHcount"]]

+    }

+)

+

@@ -135,7 +135,7 @@ A splicing graph is a directed acyclic graph (DAG) where:

 \begin{itemize}

   \item The vertices (a.k.a. \textit{nodes}) represent the splicing sites

         for a given gene. Splicing sites are numbered from $1$ to $n$

-        based on their order of appearance when moving in the 5' to 3'

+        based on the order they occur when moving in the 5' to 3'

         direction along the strand where the transcripts are located.

         Note that splicing graphs are only defined for genes that have all

         the exons of all their transcripts on the same chromosome and

@@ -337,12 +337,12 @@ elementLengths(sg)[1:20]

 @

 \Rfunction{elementLengths} is a core accessor for list-like objects

-that returns

+that returns the lengths of the individual list elements.

 At this point you might wonder why \Rfunction{elementLengths} works on

-\Rclass{SplicingGraphs} object. Does this mean that those objects are

+\Rclass{SplicingGraphs} objects. Does this mean that those objects are

 list-like objects? The answer is yes. The next thing you might wonder

-is what do the list elements look like and how can I access them?

+is what do the list elements look like and how you can access them.

 This is answered in the next subsection.

 \subsection{Basic manipulation of a \Rclass{SplicingGraphs} object}

@@ -350,8 +350,8 @@ This is answered in the next subsection.

 The list elements of a list-like object can be accessed \textbf{one at a

 time} with \Rfunction{[[}. On a \Rclass{SplicingGraphs} object, this will

 extract the transcripts of a given gene. More precisely it will return

-an \emph{unnamed} \Rclass{GRangesList} object containing the exons grouped

-by transcript:

+an \emph{unnamed} \Rclass{GRangesList} object containing the exons of the

+gene grouped by transcript:

 \begin{small}

 <<sg_double_bracket_107328>>=

@@ -364,29 +364,33 @@ The exon-level metadata columns are:

   \item \Rcode{exon\_id}: The original internal exon id as stored in the

         \Rclass{TranscriptDb} object. This id was created and assigned to

         each exon when the \Rclass{TranscriptDb} object was created.

-        It's not a public id like, say, an Ensembl, RefSeq, or GenBank id,

-        and it's only guaranteed to be unique within a \Rclass{TranscriptDb}

-        object.

+        It's not a public id like, say, an Ensembl, RefSeq, or GenBank id.

+        Furthermore, it's only guaranteed to be unique within a

+        \Rclass{TranscriptDb} object.

   \item \Rcode{exon\_name}: The original exon name as provided by the

         annotation resource (e.g. UCSC, Ensembl, or GFF file) and stored

         in the \Rclass{TranscriptDb} object when it was created.

-        \Rcode{NA} if no exon name was provided.

+        Set to \Rcode{NA} if no exon name was provided.

   \item \Rcode{exon\_rank}: The rank of the exon in the transcript.

   \item \Rcode{start\_SSid}, \Rcode{end\_SSid}: The ids of the splicing

-        sites corresponding to the start and end coordinates of the exon.

+        sites (a.k.a. \textit{Splicing Site ids}) corresponding to the

+        \textit{start} and \textit{end} coordinates of the exon.

+        (Please be cautious to not misinterpret the meaning of \textit{start}

+        and \textit{end} here. See IMPORTANT NOTE below.)

         Those ids were assigned by the \Rfunction{SplicingGraphs} constructor.

-        IMPORTANT NOTE: Please keep in mind that the start and end

-        coordinates of an exon, like the start and end coordinates of

-        a genomic range in general, are following the almost universal

-        convention that $start$ is $<= end$, and this \textbf{regardless

-        of the direction of transcription}.

 \end{itemize}

-As mentioned previously, the splicing site ids are assigned based on their

-order of appearance when moving in the 5' to 3' direction along the strand

+IMPORTANT NOTE: Please be aware that the \textit{start} and \textit{end}

+coordinates of an exon, like the \textit{start} and \textit{end}

+coordinates of a genomic range in general, are following the almost

+universal convention that \textit{start} is $<=$ \textit{end}, and this

+\textbf{regardless of the direction of transcription}.

+

+As mentioned previously, the \textit{Splicing Site ids} are assigned based

+on the order they occur when moving in the 5' to 3' direction along the strand

 of the gene. This means that, for a gene on the plus (resp. minus) strand,

 the ids in the \Rcode{start\_SSid} metadata column are always lower (resp.

-greater) than those in the \Rcode{end\_SSid} metadata column:

+greater) than those in the \Rcode{end\_SSid} metadata column.

 \begin{small}

 <<sg_double_bracket_104252>>=

@@ -394,7 +398,7 @@ sg[["104252"]]

 @

 \end{small}

-However, on both strands, the splicing site id increases with the

+However, on both strands, the \textit{Splicing Site id} increases with the

 rank of the exon.

 The \Rfunction{show} method for \Rclass{GRangesList} objects only

@@ -412,20 +416,27 @@ The transcript-level metadata columns are:

   \item \Rcode{tx\_id}: The original transcript id as provided by the

         annotation resource (e.g. UCSC, Ensembl, or GFF file) and stored

         in the \Rclass{TranscriptDb} object when it was created.

-  \item \Rcode{txpaths}: A named list-like object with one list element

-        per transcript. Each list element is an integer vector that

-        describes the \textit{path} of the transcript i.e. the splicing

-        site ids that it goes thru.

+  \item \Rcode{txpath}: A named list-like object with one list element

+        per transcript in the gene. Each list element is an integer vector

+        that describes the \textit{path} of the transcript i.e. the

+        \textit{Splicing Site ids} that it goes thru.

 \end{itemize}

 <<mcols_sg_double_bracket_107328>>=

-mcols(sg[["107328"]])$txpaths

-mcols(sg[["104252"]])$txpaths

+mcols(sg[["107328"]])$txpath

+mcols(sg[["104252"]])$txpath

+@

+

+A more convenient way to extract this information is to use the

+\Rfunction{txpath} accessor:

+

+<<txpath_sg_104252>>=

+txpath(sg[["104252"]])

 @

-Note that the list elements of the \Rcode{txpaths} metadata column

-always consist of an even number of splicing site ids in ascending

-order.

+Note that the list elements of the \Rcode{txpath} metadata column

+always consist of an even number of \textit{Splicing Site ids} in

+ascending order.

 The transcripts in a \Rclass{GRangesList} object like \Rcode{sg[["107328"]]}

 can be plotted with \Rfunction{plotTranscripts}:

Binary files a/inst/doc/precomputed_results/sg.rda and b/inst/doc/precomputed_results/sg.rda differ

Binary files a/inst/doc/precomputed_results/sg50.rda and b/inst/doc/precomputed_results/sg50.rda differ

@@ -6,9 +6,9 @@

 \alias{class:SplicingGraphs}

 \alias{SplicingGraphs-class}

-\alias{SplicingGraphs}

-\alias{SplicingGraphs,GRangesList-method}

-\alias{SplicingGraphs,TranscriptDb-method}

+\alias{seqnames,.SplicingGraphGenes-method}

+\alias{strand,.SplicingGraphGenes-method}

+\alias{seqinfo,.SplicingGraphGenes-method}

 \alias{length,SplicingGraphs-method}

 \alias{names,SplicingGraphs-method}

@@ -27,6 +27,10 @@

 \alias{plotTranscripts,TranscriptDb-method}

 \alias{plotTranscripts,SplicingGraphs-method}

+\alias{SplicingGraphs}

+\alias{SplicingGraphs,GRangesList-method}

+\alias{SplicingGraphs,TranscriptDb-method}

+

 \title{

   SplicingGraphs objects

@@ -181,6 +185,9 @@ plotTranscripts(x)

     \item \code{\link{sgedgesByTranscript}} for extracting all the introns

           or splicing graph edges from a SplicingGraphs object.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

           splicing graph.

@@ -50,6 +50,9 @@ ASCODE2DESC

     \item \code{\link{sgedgesByTranscript}} for extracting all the introns

           or splicing graph edges from a \link{SplicingGraphs} object.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

           splicing graph.

@@ -58,6 +58,9 @@ countReads(sg)

     \item \code{\link{sgedgesByTranscript}} for extracting all the introns

           or splicing graph edges from a \link{SplicingGraphs} object.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

           splicing graph.

@@ -2,12 +2,6 @@

 \alias{sgedges-methods}

-\alias{txpaths}

-\alias{txpaths,SplicingGraphs-method}

-

-\alias{UATXHcount}

-\alias{UATXHcount,SplicingGraphs-method}

-

 \alias{sgedges}

 \alias{sgedges,SplicingGraphs-method}

 \alias{sgedges,IntegerList-method}

@@ -51,10 +45,7 @@ indeg(x)

 sgedges2(x)

-## Related utilities:

-

-txpaths(x, as.matrix=FALSE)

-UATXHcount(x)

+## Related utility:

 uninformativeSSids(x)

 }

@@ -68,9 +59,6 @@ uninformativeSSids(x)

   \item{keep.dup.edges}{

     TODO

   }

-  \item{as.matrix}{

-    TODO

-  }

 }

 \details{

@@ -92,6 +80,9 @@ uninformativeSSids(x)

     \item \code{\link{sgedgesByTranscript}} for extracting all the introns

           or splicing graph edges from a \link{SplicingGraphs} object.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgraph}} for extracting a splicing graph as a

           plottable graph-like object.

@@ -114,9 +105,6 @@ sgnodes(sg["geneD"])

 outdeg(sg["geneD"])

 indeg(sg["geneD"])

-txpaths(sg["geneD"])

-txpaths(sg["geneD"], as.matrix=TRUE)  # splicing matrix

-

 ## Sanity check:

 geneD_sgedges1 <- sgedges(sg["geneD"], keep.dup.edges=TRUE)

 geneD_sgedges1 <- geneD_sgedges1[geneD_sgedges1$ex_or_in != "", ]

@@ -53,6 +53,9 @@ sgedgesByTranscript(x)

   \itemize{

     \item The \link{SplicingGraphs} class.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

           splicing graph.

@@ -70,6 +70,9 @@ slideshow(x)

     \item \code{\link{sgedgesByTranscript}} for extracting all the introns

           or splicing graph edges from a \link{SplicingGraphs} object.

+    \item \code{\link{txpath}} for extracting the transcript paths of a

+          splicing graph.

+

     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

           splicing graph.

new file mode 100644

@@ -0,0 +1,88 @@

+\name{txpath-methods}

+

+\alias{txpath-methods}

+

+\alias{txpath}

+\alias{txpath,GRangesList-method}

+\alias{txpath,SplicingGraphs-method}

+

+\alias{UATXHcount}

+\alias{UATXHcount,SplicingGraphs-method}

+

+

+\title{

+  Extract the transcript paths of a splicing graph

+}

+

+\description{

+  \code{txpath} extracts the transcript paths of the splicing graph

+  of a given gene from a \link{SplicingGraphs} object.

+}

+

+\usage{

+txpath(x, as.matrix=FALSE)

+

+## Related utility:

+UATXHcount(x)

+}

+

+\arguments{

+  \item{x}{

+    A \link{SplicingGraphs} object of length 1

+    or a \link[GenomicRanges]{GRangesList} object.

+  }

+  \item{as.matrix}{

+    TODO

+  }

+}

+

+\details{

+  TODO

+}

+

+\value{

+  A named list-like object with one list element per transcript in the gene.

+  Each list element is an integer vector that describes the \emph{path}

+  of the transcript i.e. the \emph{Splicing Site ids} that it goes thru.

+}

+

+\author{

+  H. Pages

+}

+

+\seealso{

+  \itemize{

+    \item The \link{SplicingGraphs} class.

+

+    \item \code{\link{sgedgesByTranscript}} for extracting all the introns

+          or splicing graph edges from a \link{SplicingGraphs} object.

+

+    \item \code{\link{sgedges}} for extracting the edges (and nodes) of a

+          splicing graph.

+

+    \item \code{\link{sgraph}} for extracting a splicing graph as a

+          plottable graph-like object.

+

+    \item \code{\link{bubbles}} for computing the bubbles of a splicing graph.

+

+    \item \code{\link{countReads}} for assigning reads to a

+          \link{SplicingGraphs} object and counting them.

+  }

+}

+

+\examples{

+example(SplicingGraphs)  # create SplicingGraphs object 'sg'

+sg

+

+## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids.

+names(sg)

+

+## Note that the list elements in the returned IntegerList object

+## always consist of an even number of Splicing Site ids in ascending

+## order.

+txpath(sg["geneB"])

+txpath(sg["geneD"])

+strand(sg)

+

+txpath(sg["geneD"], as.matrix=TRUE)  # splicing matrix

+}