1. SplicingGraphs
  2. NAMESPACE
Browse code

SplicingGraphs 1.49.1: Replace GenomeInfoDb with Seqinfo

Hervé Pagès authored on 24/07/2025 23:12:12
Showing 1 changed files
NAMESPACE
History View file @ c006477
... ... 
@@ -11,7 +11,7 @@ import(BiocGenerics)
11 11 
 import(S4Vectors)
12 12 
 import(BiocParallel)
13 13 
 import(IRanges)
14 
-import(GenomeInfoDb)
14 
+import(Seqinfo)
15 15 
 import(GenomicRanges)
16 16 
 import(GenomicFeatures)
17 17 
 importFrom(Rsamtools, asBam)
... ... 
@@ -54,7 +54,7 @@ exportMethods(
54 54 
     ## Methods for generics defined in the S4Vectors package:
55 55 
     elementNROWS,
56 56
57 
-    ## Methods for generics defined in the GenomeInfoDb package:
57 
+    ## Methods for generics defined in the Seqinfo package:
58 58 
     seqnames, seqinfo, "isCircular<-",
59 59
60 60 
     ## Methods for generics defined in the GenomicFeatures package:
Browse code

Add new txdbmaker package to Suggests

Hervé Pagès authored on 18/03/2024 17:15:15
Showing 1 changed files
NAMESPACE
History View file @ 92376aa
... ... 
@@ -1,5 +1,5 @@
1 1 
 import(methods)
2 
-import(utils)
2 
+importFrom(utils, read.table)
3 3 
 importFrom(graphics, plot)
4 4
5 5 
 importFrom(igraph, vcount, vertex_attr, ecount, edge_attr, as_edgelist,
Browse code

Repair internal utility make_Ragraph_from_igraph()

It broke because of a recent change to igraph::igraph.to.graphNEL().

Hervé Pagès authored on 14/04/2023 02:02:42
Showing 1 changed files
NAMESPACE
History View file @ 6078cfa
... ... 
@@ -2,8 +2,9 @@ import(methods)
2 2 
 import(utils)
3 3 
 importFrom(graphics, plot)
4 4
5 
-importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
6 
-                   plot.igraph, igraph.to.graphNEL)
5 
+importFrom(igraph, vcount, vertex_attr, ecount, edge_attr, as_edgelist,
6 
+                   is_directed, graph.data.frame, get.data.frame,
7 
+                   layout.kamada.kawai, plot.igraph, igraph.to.graphNEL)
7 8
8 9
9 10 
 import(BiocGenerics)
... ... 
@@ -19,7 +20,7 @@ import(GenomicAlignments)
19 20 
 importFrom(graph, nodeDataDefaults, nodeData,
20 21 
                   edgeDataDefaults, edgeNames, edgeData, edgemode)
21 22
22 
-importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
23 
+importFrom(Rgraphviz, agopen)
23 24 
 importMethodsFrom(Rgraphviz, plot)
24 25
25 26
Browse code

Add updateObject() method for SplicingGraphs objects

Hervé Pagès authored on 20/11/2019 05:45:12
Showing 1 changed files
NAMESPACE
History View file @ 8aa1a42
... ... 
@@ -22,6 +22,11 @@ importFrom(graph, nodeDataDefaults, nodeData,
22 22 
 importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
23 23 
 importMethodsFrom(Rgraphviz, plot)
24 24
25 
+
26 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
27 
+### Export S4 classes
28 
+###
29 
+
25 30 
 exportClasses(GeneModel, SplicingGraphs)
26 31
27 32
... ... 
@@ -30,18 +35,29 @@ exportClasses(GeneModel, SplicingGraphs)
30 35 
 ###
31 36
32 37 
 exportMethods(
33 
-    length,
34 
-    names,
35 
-    show,
36 
-    "[",
37 
-    "[[",
38 
-    elementNROWS,
38 
+    ## Methods for generics defined in the base package:
39 
+    length, names,
40 
+    "[", "[[",
39 41 
     unlist,
40 
-    seqnames,
42 
+
43 
+    ## Methods for generics defined in the methods package:
44 
+    show,
45 
+
46 
+    ## Methods for generics defined in the graphics package:
47 
+    plot,
48 
+
49 
+    ## Methods for generics defined in the BiocGenerics package:
41 50 
     strand,
42 
-    seqinfo, "isCircular<-",
43 
-    intronsByTranscript,
44 
-    plot
51 
+    updateObject,
52 
+
53 
+    ## Methods for generics defined in the S4Vectors package:
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+    elementNROWS,
55 
+
56 
+    ## Methods for generics defined in the GenomeInfoDb package:
57 
+    seqnames, seqinfo, "isCircular<-",
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+
59 
+    ## Methods for generics defined in the GenomicFeatures package:
60 
+    intronsByTranscript
45 61 
 )
46 62
47 63
Browse code

Use gene 7597 instead of 100309464 in vignette

Hervé Pagès authored on 29/01/2019 01:53:53
Showing 1 changed files
NAMESPACE
History View file @ 7041582
... ... 
@@ -8,6 +8,7 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
8 8
9 9 
 import(BiocGenerics)
10 10 
 import(S4Vectors)
11 
+import(BiocParallel)
11 12 
 import(IRanges)
12 13 
 import(GenomeInfoDb)
13 14 
 import(GenomicRanges)
Browse code

Dispatch on the appropriate plot method was failing because I forgot to import the plot methods from Rgraphviz. Fixed.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@122709 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:41:03
Showing 1 changed files
NAMESPACE
History View file @ f520787
... ... 
@@ -19,6 +19,7 @@ importFrom(graph, nodeDataDefaults, nodeData,
19 19 
                   edgeDataDefaults, edgeNames, edgeData, edgemode)
20 20
21 21 
 importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
22 
+importMethodsFrom(Rgraphviz, plot)
22 23
23 24 
 exportClasses(GeneModel, SplicingGraphs)
24 25
Browse code

import plot() from graphics

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@119308 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 12/07/2016 09:29:28
Showing 1 changed files
NAMESPACE
History View file @ 4abd277
... ... 
@@ -1,5 +1,6 @@
1 1 
 import(methods)
2 2 
 import(utils)
3 
+importFrom(graphics, plot)
3 4
4 5 
 importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
5 6 
                    plot.igraph, igraph.to.graphNEL)
Browse code

use elementNROWS() instead of elementLengths()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@112988 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/01/2016 09:05:43
Showing 1 changed files
NAMESPACE
History View file @ 09cffc8
... ... 
@@ -32,7 +32,7 @@ exportMethods(
32 32 
     show,
33 33 
     "[",
34 34 
     "[[",
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-    elementLengths,
35 
+    elementNROWS,
36 36 
     unlist,
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     seqnames,
38 38 
     strand,
Browse code

fix vignette failure caused by update to TxDb.Hsapiens.UCSC.hg19.knownGene

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@107854 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/08/2015 00:08:25
Showing 1 changed files
NAMESPACE
History View file @ a3a942c
... ... 
@@ -36,7 +36,7 @@ exportMethods(
36 36 
     unlist,
37 37 
     seqnames,
38 38 
     strand,
39 
-    seqinfo,
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+    seqinfo, "isCircular<-",
40 40 
     intronsByTranscript,
41 41 
     plot
42 42 
 )
Browse code

Rsamtools is now required instead of suggested only

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@98136 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/01/2015 20:07:56
Showing 1 changed files
NAMESPACE
History View file @ 1d57ccf
... ... 
@@ -11,6 +11,7 @@ import(IRanges)
11 11 
 import(GenomeInfoDb)
12 12 
 import(GenomicRanges)
13 13 
 import(GenomicFeatures)
14 
+importFrom(Rsamtools, asBam)
14 15 
 import(GenomicAlignments)
15 16
16 17 
 importFrom(graph, nodeDataDefaults, nodeData,
Browse code

add a few missing imports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@98054 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/01/2015 07:58:11
Showing 1 changed files
NAMESPACE
History View file @ 00ea746
... ... 
@@ -8,14 +8,15 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
8 8 
 import(BiocGenerics)
9 9 
 import(S4Vectors)
10 10 
 import(IRanges)
11 
+import(GenomeInfoDb)
11 12 
 import(GenomicRanges)
12 13 
 import(GenomicFeatures)
13 14 
 import(GenomicAlignments)
14 15
15 16 
 importFrom(graph, nodeDataDefaults, nodeData,
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-                  edgeDataDefaults, edgeNames, edgeData)
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+                  edgeDataDefaults, edgeNames, edgeData, edgemode)
17 18
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-importFrom(Rgraphviz, agopen)
19 
+importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
19 20
20 21 
 exportClasses(GeneModel, SplicingGraphs)
21 22
Browse code

resync with stuff moving from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@89259 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 19/04/2014 21:10:47
Showing 1 changed files
NAMESPACE
History View file @ ab34260
... ... 
@@ -6,7 +6,7 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
6 6
7 7
8 8 
 import(BiocGenerics)
9 
-
9 
+import(S4Vectors)
10 10 
 import(IRanges)
11 11 
 import(GenomicRanges)
12 12 
 import(GenomicFeatures)
Browse code

need to import new GenomicAlignments package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@84015 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/12/2013 06:04:19
Showing 1 changed files
NAMESPACE
History View file @ 05644e5
... ... 
@@ -10,6 +10,7 @@ import(BiocGenerics)
10 10 
 import(IRanges)
11 11 
 import(GenomicRanges)
12 12 
 import(GenomicFeatures)
13 
+import(GenomicAlignments)
13 14
14 15 
 importFrom(graph, nodeDataDefaults, nodeData,
15 16 
                   edgeDataDefaults, edgeNames, edgeData)
Browse code

Export "show" method.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@80627 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 21/09/2013 02:10:46
Showing 1 changed files
NAMESPACE
History View file @ 48887b0
... ... 
@@ -26,6 +26,7 @@ exportClasses(GeneModel, SplicingGraphs)
26 26 
 exportMethods(
27 27 
     length,
28 28 
     names,
29 
+    show,
29 30 
     "[",
30 31 
     "[[",
31 32 
     elementLengths,
Browse code

- Rename getReads() -> reportReads(). - Complete man page for countReads()/reportReads().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76132 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/04/2013 22:07:38
Showing 1 changed files
NAMESPACE
History View file @ 189b61d
... ... 
@@ -102,7 +102,7 @@ export(
102 102 
     bubbles,
103 103
104 104 
     ## countReads-methods.R:
105 
-    getReads,
105 
+    reportReads,
106 106 
     countReads
107 107 
 )
108 108
... ... 
@@ -122,7 +122,7 @@ exportMethods(
122 122 
     rsgedgesByTranscript,
123 123 
     rsgedgesByGene,
124 124 
     bubbles,
125 
-    getReads,
125 
+    reportReads,
126 126 
     countReads
127 127 
 )
128 128
Browse code

Add getReads(). Similar to countReads() but returns right before the final counting step, that is, the returned DataFrame contains the reads instead of their counts.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76127 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/04/2013 18:02:30
Showing 1 changed files
NAMESPACE
History View file @ 05410e1
... ... 
@@ -102,6 +102,7 @@ export(
102 102 
     bubbles,
103 103
104 104 
     ## countReads-methods.R:
105 
+    getReads,
105 106 
     countReads
106 107 
 )
107 108
... ... 
@@ -121,6 +122,7 @@ exportMethods(
121 122 
     rsgedgesByTranscript,
122 123 
     rsgedgesByGene,
123 124 
     bubbles,
125 
+    getReads,
124 126 
     countReads
125 127 
 )
126 128
Browse code

- Move Rsamtools from Imports to Suggests. - Add .Rinstignore file. - Add some biocViews terms.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76094 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 27/04/2013 06:43:14
Showing 1 changed files
NAMESPACE
History View file @ b129389
... ... 
@@ -6,17 +6,16 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
6 6
7 7
8 8 
 import(BiocGenerics)
9 
+
9 10 
 import(IRanges)
10 11 
 import(GenomicRanges)
12 
+import(GenomicFeatures)
11 13
12 14 
 importFrom(graph, nodeDataDefaults, nodeData,
13 15 
                   edgeDataDefaults, edgeNames, edgeData)
14 16
15 17 
 importFrom(Rgraphviz, agopen)
16 18
17 
-import(GenomicFeatures)
18 
-import(Rsamtools)
19 
-
20 19 
 exportClasses(GeneModel, SplicingGraphs)
21 20
22 21
Browse code

Split countReads-methods.R into 2 units: assignReads.R and countReads-methods.R

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76089 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 26/04/2013 22:47:35
Showing 1 changed files
NAMESPACE
History View file @ 75d6518
... ... 
@@ -54,7 +54,7 @@ export(
54 54 
     ## bubbles-methods.R:
55 55 
     ASCODE2DESC,
56 56
57 
-    ## countReads-methods.R:
57 
+    ## assignReads.R:
58 58 
     assignReads,
59 59 
     removeReads,
60 60
Browse code

Starting unit tests + other minor tweaks.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76087 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 26/04/2013 22:09:30
Showing 1 changed files
NAMESPACE
History View file @ 94444bd
... ... 
@@ -54,7 +54,7 @@ export(
54 54 
     ## bubbles-methods.R:
55 55 
     ASCODE2DESC,
56 56
57 
-    ## countReads.R:
57 
+    ## countReads-methods.R:
58 58 
     assignReads,
59 59 
     removeReads,
60 60
... ... 
@@ -102,7 +102,7 @@ export(
102 102 
     ## bubbles-methods.R:
103 103 
     bubbles,
104 104
105 
-    ## countReads.R:
105 
+    ## countReads-methods.R:
106 106 
     countReads
107 107 
 )
108 108
Browse code

Complete sgedgesByGene-methods.Rd man page.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76074 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 26/04/2013 17:45:22
Showing 1 changed files
NAMESPACE
History View file @ a48698e
... ... 
@@ -17,7 +17,7 @@ importFrom(Rgraphviz, agopen)
17 17 
 import(GenomicFeatures)
18 18 
 import(Rsamtools)
19 19
20 
-exportClasses(.SplicingGraphGenes, SplicingGraphs)
20 
+exportClasses(GeneModel, SplicingGraphs)
21 21
22 22
23 23 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Browse code

- Add removeReads() for removing all the reads assigned to a SplicingGraphs object. - Use all.equal() instead of identical() for comparing SplicingGraphs objects. - Update precomputed SplicingGraphs objects used in the vignette.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@76059 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 26/04/2013 09:15:46
Showing 1 changed files
NAMESPACE
History View file @ 650ba9d
... ... 
@@ -56,6 +56,7 @@ export(
56 56
57 57 
     ## countReads.R:
58 58 
     assignReads,
59 
+    removeReads,
59 60
60 61 
     ## toy_data.R:
61 62 
     toy_genes_gff,
Browse code

Add man page for rsgedgesByGene() and family.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75782 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/04/2013 19:50:29
Showing 1 changed files
NAMESPACE
History View file @ 9ce7e84
... ... 
@@ -47,6 +47,10 @@ export(
47 47 
     ## sgraph-methods.R:
48 48 
     slideshow,
49 49
50 
+    ## rsgedgesByGene-methods.R:
51 
+    rsgedges, sgedges2,
52 
+    rsgraph, sgraph2,
53 
+
50 54 
     ## bubbles-methods.R:
51 55 
     ASCODE2DESC,
52 56
... ... 
@@ -89,15 +93,13 @@ export(
89 93 
     ## sgraph-methods.R:
90 94 
     sgraph,
91 95
92 
-    ## bubbles-methods.R:
93 
-    bubbles,
94 
-
95 96 
     ## rsgedgesByGene-methods.R:
96 97 
     uninformativeSSids,
97 98 
     rsgedgesByTranscript,
98 99 
     rsgedgesByGene,
99 
-    rsgedges, sgedges2,
100 
-    rsgraph, sgraph2,
100 
+
101 
+    ## bubbles-methods.R:
102 
+    bubbles,
101 103
102 104 
     ## countReads.R:
103 105 
     countReads
... ... 
@@ -114,11 +116,11 @@ exportMethods(
114 116 
     sgedges,
115 117 
     sgnodes,
116 118 
     outdeg, indeg,
117 
-    uninformativeSSids,
118 119 
     sgraph,
119 
-    bubbles,
120 
+    uninformativeSSids,
120 121 
     rsgedgesByTranscript,
121 122 
     rsgedgesByGene,
123 
+    bubbles,
122 124 
     countReads
123 125 
 )
124 126
Browse code

o Move sgedges2(), uninformativeSSids(), and sgraph2() to R/rsgedgesByGene-methods.R o Rename sgedges2() -> rgedges() and sgraph2() -> rsgraph(). Keep old names as aliases to new names.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75704 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/04/2013 17:59:45
Showing 1 changed files
NAMESPACE
History View file @ 0861db8
... ... 
@@ -44,11 +44,7 @@ exportMethods(
44 44 
 ###
45 45
46 46 
 export(
47 
-    ## sgedges-methods.R:
48 
-    sgedges2,
49 
-
50 47 
     ## sgraph-methods.R:
51 
-    sgraph2,
52 48 
     slideshow,
53 49
54 50 
     ## bubbles-methods.R:
... ... 
@@ -89,7 +85,6 @@ export(
89 85 
     sgedges,
90 86 
     sgnodes,
91 87 
     outdeg, indeg,
92 
-    uninformativeSSids,
93 88
94 89 
     ## sgraph-methods.R:
95 90 
     sgraph,
... ... 
@@ -98,8 +93,11 @@ export(
98 93 
     bubbles,
99 94
100 95 
     ## rsgedgesByGene-methods.R:
96 
+    uninformativeSSids,
101 97 
     rsgedgesByTranscript,
102 98 
     rsgedgesByGene,
99 
+    rsgedges, sgedges2,
100 
+    rsgraph, sgraph2,
103 101
104 102 
     ## countReads.R:
105 103 
     countReads
Browse code

countReads() now allows counting by *reduced* splicing graph edge in addition to counting by splicing graph edge. This is controlled via the new 'by' argument.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75609 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 12/04/2013 17:59:17
Showing 1 changed files
NAMESPACE
History View file @ c10df4d
... ... 
@@ -56,7 +56,6 @@ export(
56 56
57 57 
     ## countReads.R:
58 58 
     assignReads,
59 
-    countReads,
60 59
61 60 
     ## toy_data.R:
62 61 
     toy_genes_gff,
... ... 
@@ -100,7 +99,10 @@ export(
100 99
101 100 
     ## rsgedgesByGene-methods.R:
102 101 
     rsgedgesByTranscript,
103 
-    rsgedgesByGene
102 
+    rsgedgesByGene,
103 
+
104 
+    ## countReads.R:
105 
+    countReads
104 106 
 )
105 107
106 108 
 ### Exactly the same list as above.
... ... 
@@ -118,6 +120,7 @@ exportMethods(
118 120 
     sgraph,
119 121 
     bubbles,
120 122 
     rsgedgesByTranscript,
121 
-    rsgedgesByGene
123 
+    rsgedgesByGene,
124 
+    countReads
122 125 
 )
123 126
Browse code

Add rsgedgesByGene().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75596 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 12/04/2013 07:04:39
Showing 1 changed files
NAMESPACE
History View file @ 43e1ae9
... ... 
@@ -96,7 +96,11 @@ export(
96 96 
     sgraph,
97 97
98 98 
     ## bubbles-methods.R:
99 
-    bubbles
99 
+    bubbles,
100 
+
101 
+    ## rsgedgesByGene-methods.R:
102 
+    rsgedgesByTranscript,
103 
+    rsgedgesByGene
100 104 
 )
101 105
102 106 
 ### Exactly the same list as above.
... ... 
@@ -112,6 +116,8 @@ exportMethods(
112 116 
     outdeg, indeg,
113 117 
     uninformativeSSids,
114 118 
     sgraph,
115 
-    bubbles
119 
+    bubbles,
120 
+    rsgedgesByTranscript,
121 
+    rsgedgesByGene
116 122 
 )
117 123
Browse code

- Rename UATXHcount() accessor -> txweight(). - Add txweight() setter for SplicingGraphs objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75217 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 03/04/2013 07:25:30
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NAMESPACE
History View file @ 475e101
... ... 
@@ -84,7 +84,7 @@ export(
84 84
85 85 
     ## txpath-methods.R:
86 86 
     txpath,
87 
-    UATXHcount,
87 
+    txweight, "txweight<-",
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     ## sgedges-methods.R:
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     sgedges,
... ... 
@@ -106,7 +106,7 @@ exportMethods(
106 106 
     sgedgesByTranscript,
107 107 
     sgedgesByGene,
108 108 
     txpath,
109 
-    UATXHcount,
109 
+    txweight, "txweight<-",
110 110 
     sgedges,
111 111 
     sgnodes,
112 112 
     outdeg, indeg,
Browse code

- Add 'reads', 'from', and 'to' args to plotTranscripts(). - Remove plotToyReads().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75215 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 03/04/2013 05:09:07
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NAMESPACE
History View file @ 2c9e1ed
... ... 
@@ -62,8 +62,7 @@ export(
62 62 
     toy_genes_gff,
63 63 
     toy_reads_sam,
64 64 
     toy_reads_bam,
65 
-    toy_overlaps,
66 
-    plotToyReads
65 
+    toy_overlaps
67 66 
 )
68 67
69 68
Browse code

Move plotTranscripts() to its own .R and .Rd files.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75209 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 02/04/2013 23:43:51
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NAMESPACE
History View file @ d52043c
... ... 
@@ -74,9 +74,11 @@ export(
74 74
75 75 
 export(
76 76 
     ## SplicingGraphs-class.R:
77 
-    plotTranscripts,
78 77 
     SplicingGraphs,
79 78
79 
+    ## plotTranscripts-methods.R:
80 
+    plotTranscripts,
81 
+
80 82 
     ## sgedgesByGene-methods.R:
81 83 
     sgedgesByTranscript,
82 84 
     sgedgesByGene,
... ... 
@@ -100,8 +102,8 @@ export(
100 102
101 103 
 ### Exactly the same list as above.
102 104 
 exportMethods(
103 
-    plotTranscripts,
104 105 
     SplicingGraphs,
106 
+    plotTranscripts,
105 107 
     sgedgesByTranscript,
106 108 
     sgedgesByGene,
107 109 
     txpath,
Browse code

- Add 'keep.dup.edges' arg to sgedgesByGene(). - Fix and optimize countReads(). Current version is about 70x faster than initial version.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75118 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 31/03/2013 20:53:22
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NAMESPACE
History View file @ 942a590
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@@ -77,7 +77,7 @@ export(
77 77 
     plotTranscripts,
78 78 
     SplicingGraphs,
79 79
80 
-    ## sgedgesByTranscript-methods.R:
80 
+    ## sgedgesByGene-methods.R:
81 81 
     sgedgesByTranscript,
82 82 
     sgedgesByGene,
83 83
Browse code

- Add 'keep.exon.mcols' and 'keep.hits.mcols' to sgedgesByTranscript(). - Add sgedgesByGene().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75107 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 31/03/2013 09:39:48
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NAMESPACE
History View file @ 9cd225c
... ... 
@@ -79,6 +79,7 @@ export(
79 79
80 80 
     ## sgedgesByTranscript-methods.R:
81 81 
     sgedgesByTranscript,
82 
+    sgedgesByGene,
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83 84 
     ## txpath-methods.R:
84 85 
     txpath,
... ... 
@@ -102,6 +103,7 @@ exportMethods(
102 103 
     plotTranscripts,
103 104 
     SplicingGraphs,
104 105 
     sgedgesByTranscript,
106 
+    sgedgesByGene,
105 107 
     txpath,
106 108 
     UATXHcount,
107 109 
     sgedges,
Browse code

Renamed txpaths() -> txpath().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@75014 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/03/2013 22:58:26
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NAMESPACE
History View file @ 7ff5c4a
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@@ -80,9 +80,11 @@ export(
80 80 
     ## sgedgesByTranscript-methods.R:
81 81 
     sgedgesByTranscript,
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83 
-    ## sgedges-methods.R:
84 
-    txpaths,
83 
+    ## txpath-methods.R:
84 
+    txpath,
85 85 
     UATXHcount,
86 
+
87 
+    ## sgedges-methods.R:
86 88 
     sgedges,
87 89 
     sgnodes,
88 90 
     outdeg, indeg,
... ... 
@@ -100,7 +102,7 @@ exportMethods(
100 102 
     plotTranscripts,
101 103 
     SplicingGraphs,
102 104 
     sgedgesByTranscript,
103 
-    txpaths,
105 
+    txpath,
104 106 
     UATXHcount,
105 107 
     sgedges,
106 108 
     sgnodes,
Browse code

Add "seqinfo" accessor for SplicingGraphs objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74997 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/03/2013 19:46:24
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NAMESPACE
History View file @ 66886f4
... ... 
@@ -33,6 +33,7 @@ exportMethods(
33 33 
     unlist,
34 34 
     seqnames,
35 35 
     strand,
36 
+    seqinfo,
36 37 
     intronsByTranscript,
37 38 
     plot
38 39 
 )
Browse code

Add "seqnames" and "strand" methods for SplicingGraphs objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74984 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/03/2013 17:59:02
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NAMESPACE
History View file @ 937fc96
... ... 
@@ -31,6 +31,8 @@ exportMethods(
31 31 
     "[[",
32 32 
     elementLengths,
33 33 
     unlist,
34 
+    seqnames,
35 
+    strand,
34 36 
     intronsByTranscript,
35 37 
     plot
36 38 
 )
Browse code

Add countReads().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74917 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 27/03/2013 09:16:34
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NAMESPACE
History View file @ 714c936
... ... 
@@ -53,6 +53,7 @@ export(
53 53
54 54 
     ## countReads.R:
55 55 
     assignReads,
56 
+    countReads,
56 57
57 58 
     ## toy_data.R:
58 59 
     toy_genes_gff,
Browse code

Add sgedgesByTranscript() extractor.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74898 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 27/03/2013 00:34:42
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NAMESPACE
History View file @ 6c1f410
... ... 
@@ -73,6 +73,9 @@ export(
73 73 
     plotTranscripts,
74 74 
     SplicingGraphs,
75 75
76 
+    ## sgedgesByTranscript-methods.R:
77 
+    sgedgesByTranscript,
78 
+
76 79 
     ## sgedges-methods.R:
77 80 
     txpaths,
78 81 
     UATXHcount,
... ... 
@@ -92,6 +95,7 @@ export(
92 95 
 exportMethods(
93 96 
     plotTranscripts,
94 97 
     SplicingGraphs,
98 
+    sgedgesByTranscript,
95 99 
     txpaths,
96 100 
     UATXHcount,
97 101 
     sgedges,
Browse code

Add assignReads() for assigning reads to a SplicingGraphs object.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74846 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 26/03/2013 15:47:17
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NAMESPACE
History View file @ 1701fd0
... ... 
@@ -52,7 +52,7 @@ export(
52 52 
     ASCODE2DESC,
53 53
54 54 
     ## countReads.R:
55 
-    assignSubfeatureHits,
55 
+    assignReads,
56 56
57 57 
     ## toy_data.R:
58 58 
     toy_genes_gff,
Browse code

Numerous tweaks to have new("SplicingGraphs") return a valid SplicingGraphs object (of length 0).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74636 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 21/03/2013 06:06:06
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NAMESPACE
History View file @ ddf79f2
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@@ -17,7 +17,7 @@ importFrom(Rgraphviz, agopen)
17 17 
 import(GenomicFeatures)
18 18 
 import(Rsamtools)
19 19
20 
-exportClasses(SplicingGraphs)
20 
+exportClasses(.SplicingGraphGenes, SplicingGraphs)
21 21
22 22
23 23 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Browse code

Add "intronsByTranscript" method for SplicingGraphs objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74563 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 19/03/2013 18:19:01
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NAMESPACE
History View file @ dd0bd6a
... ... 
@@ -31,6 +31,7 @@ exportMethods(
31 31 
     "[[",
32 32 
     elementLengths,
33 33 
     unlist,
34 
+    intronsByTranscript,
34 35 
     plot
35 36 
 )
36 37
Browse code

Add cache mechanism for the bubbles of a SplicingGraphs object.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74373 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 15/03/2013 06:59:19
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NAMESPACE
History View file @ 24537e9
... ... 
@@ -36,7 +36,7 @@ exportMethods(
36 36
37 37
38 38 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
39 
-### Export non-generic functions
39 
+### Export non-generic functions (and non-function symbols)
40 40 
 ###
41 41
42 42 
 export(
... ... 
@@ -47,6 +47,9 @@ export(
47 47 
     sgraph2,
48 48 
     slideshow,
49 49
50 
+    ## bubbles-methods.R:
51 
+    ASCODE2DESC,
52 
+
50 53 
     ## countReads.R:
51 54 
     assignSubfeatureHits,
52 55
Browse code

Add plotTranscripts().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74346 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 14/03/2013 20:12:11
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NAMESPACE
History View file @ 35dfe57
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@@ -66,6 +66,7 @@ export(
66 66
67 67 
 export(
68 68 
     ## SplicingGraphs-class.R:
69 
+    plotTranscripts,
69 70 
     SplicingGraphs,
70 71
71 72 
     ## sgedges-methods.R:
... ... 
@@ -85,6 +86,7 @@ export(
85 86
86 87 
 ### Exactly the same list as above.
87 88 
 exportMethods(
89 
+    plotTranscripts,
88 90 
     SplicingGraphs,
89 91 
     txpaths,
90 92 
     UATXHcount,
Browse code

Another change to the SplicingGraphs class definition so that only the following restricted API is available for these objects: length(), names(), [, [[, elementLengths(), and unlist(). That's all we need for now.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74197 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 11/03/2013 23:54:12
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NAMESPACE
History View file @ 69a8543
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@@ -25,6 +25,12 @@ exportClasses(SplicingGraphs)
25 25 
 ###
26 26
27 27 
 exportMethods(
28 
+    length,
29 
+    names,
30 
+    "[",
31 
+    "[[",
32 
+    elementLengths,
33 
+    unlist,
28 34 
     plot
29 35 
 )
30 36
Browse code

Change SplicingGraphs class definition and API so SplicingGraphs objects are now list-like objects with 1 gene per list element.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74180 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 11/03/2013 21:18:32
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NAMESPACE
History View file @ 7774286
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@@ -25,12 +25,7 @@ exportClasses(SplicingGraphs)
25 25 
 ###
26 26
27 27 
 exportMethods(
28 
-    length,
29 
-    names,
30 
-    elementLengths,
31 
-    plot,
32 
-    findOverlaps,
33 
-    encodeOverlaps
28 
+    plot
34 29 
 )
35 30
36 31
Browse code

Add the outdeg() and indeg() extractors.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@74055 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/03/2013 07:06:19
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NAMESPACE
History View file @ aaaabdf
... ... 
@@ -72,6 +72,7 @@ export(
72 72 
     UATXHcount,
73 73 
     sgedges,
74 74 
     sgnodes,
75 
+    outdeg, indeg,
75 76 
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77 78 
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... ... 
@@ -88,6 +89,7 @@ exportMethods(
88 89 
     UATXHcount,
89 90 
     sgedges,
90 91 
     sgnodes,
92 
+    outdeg, indeg,
91 93 
     uninformativeSSids,
92 94 
     sgraph,
93 95 
     bubbles
Browse code

Rename spath() -> txpaths().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73979 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/03/2013 20:28:00
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NAMESPACE
History View file @ 0544366
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@@ -68,7 +68,7 @@ export(
68 68 
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69 69
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     ## sgedges-methods.R:
71 
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71 
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... ... 
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84 84 
 ### Exactly the same list as above.
85 85 
 exportMethods(
86 86 
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+    txpaths,
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     UATXHcount,
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     sgedges,
90 90 
     sgnodes,
Browse code

Add bubbles() for extracting the bubbles of a splicing graph.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73962 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/03/2013 07:44:09
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NAMESPACE
History View file @ 261b473
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@@ -75,7 +75,10 @@ export(
75 75 
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     ## sgraph-methods.R:
78 
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+
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+    ## bubbles-methods.R:
81 
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 ### Exactly the same list as above.
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86 89 
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     sgnodes,
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93 
+    bubbles
90 94 
 )
91 95
Browse code

Add sgnodes() extractor.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73958 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/03/2013 01:36:15
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NAMESPACE
History View file @ f3bb380
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@@ -71,6 +71,7 @@ export(
71 71 
     spath,
72 72 
     UATXHcount,
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@@ -83,6 +84,7 @@ exportMethods(
83 84 
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     sgedges,
87 
+    sgnodes,
86 88 
     uninformativeSSids,
87 89 
     sgraph
88 90 
 )
Browse code

Rename sgdf() and sgdf2() -> sgedges() and sgedges2().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73957 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/03/2013 01:25:42
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NAMESPACE
History View file @ b72ecce
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@@ -39,8 +39,8 @@ exportMethods(
39 39 
 ###
40 40
41 41 
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42 
-    ## sgdf-methods.R:
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43 
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45 45 
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67 67 
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70 
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72 72 
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82 82 
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85 
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     uninformativeSSids,
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     sgraph
88 88 
 )
Browse code

- Make SplicingGraphs() a generic function with methods for GRangesList and TranscriptDb objects. - More progress (45%) on the vignette.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73938 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/03/2013 18:51:08
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NAMESPACE
History View file @ cb383bf
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@@ -39,9 +39,6 @@ exportMethods(
39 39 
 ###
40 40
41 41 
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42 
-    ## SplicingGraphs-class.R:
43 
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45 42 
     ## sgdf-methods.R:
46 43 
     sgdf2,
47 44
... ... 
@@ -67,6 +64,9 @@ export(
67 64 
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68 65
69 66 
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67 
+    ## SplicingGraphs-class.R:
68 
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69 
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70 70 
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71 71 
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     UATXHcount,
... ... 
@@ -79,6 +79,7 @@ export(
79 79
80 80 
 ### Exactly the same list as above.
81 81 
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82 
+    SplicingGraphs,
82 83 
     spath,
83 84 
     UATXHcount,
84 85 
     sgdf,
Browse code

o Plot exon edges in orange instead of green. o Add 'tx_id.as.edge.label' arg to sgraph() and sgraph2(). o Add slideshow().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73895 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 04/03/2013 18:14:08
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NAMESPACE
History View file @ e401803
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@@ -47,6 +47,7 @@ export(
47 47
48 48 
     ## sgraph-methods.R:
49 49 
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+    slideshow,
50 51
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     ## countReads.R:
52 53 
     assignSubfeatureHits,
Browse code

- Split SplicingGraphs-class.R in 3 files: SplicingGraphs-class.R, sgdf-methods.R, and sgraph-methods.R. And split the corresponding man page accordingly. - Rename Spath(), Sgdf(), Sgraph() -> spath(), sgdf(), sgraph().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73836 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/02/2013 21:57:06
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NAMESPACE
History View file @ 5712a4d
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@@ -19,35 +19,69 @@ import(Rsamtools)
19 19
20 20 
 exportClasses(SplicingGraphs)
21 21
22 
+
23 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
24 
+### Export S4 methods for generics not defined in SplicingGraphs
25 
+###
26 
+
27 
+exportMethods(
28 
+    length,
29 
+    names,
30 
+    elementLengths,
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+    plot,
32 
+    findOverlaps,
33 
+    encodeOverlaps
34 
+)
35 
+
36 
+
37 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
38 
+### Export non-generic functions
39 
+###
40 
+
41 
+export(
42 
+    ## SplicingGraphs-class.R:
43 
+    SplicingGraphs,
44 
+
45 
+    ## sgdf-methods.R:
46 
+    sgdf2,
47 
+
48 
+    ## sgraph-methods.R:
49 
+    sgraph2,
50 
+
51 
+    ## countReads.R:
52 
+    assignSubfeatureHits,
53 
+
54 
+    ## toy_data.R:
55 
+    toy_genes_gff,
56 
+    toy_reads_sam,
57 
+    toy_reads_bam,
58 
+    toy_overlaps,
59 
+    plotToyReads
60 
+)
61 
+
62 
+
63 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
64 
+### Export S4 generics defined in SplicingGraphs + export corresponding
65 
+### methods
66 
+###
67 
+
22 68 
 export(
23 
-  Spath,
24 
-  UATXHcount,
25 
-  Sgdf,
26 
-  Sgraph,
27 
-  uninformativeSSids,
28 
-  Sgdf2,
29 
-  Sgraph2,
30 
-  SplicingGraphs,
31 
-
32 
-  assignSubfeatureHits,
33 
-
34 
-  toy_genes_gff,
35 
-  toy_reads_sam,
36 
-  toy_reads_bam,
37 
-  toy_overlaps,
38 
-  plotToyReads
69 
+    ## sgdf-methods.R:
70 
+    spath,
71 
+    UATXHcount,
72 
+    sgdf,
73 
+    uninformativeSSids,
74 
+
75 
+    ## sgraph-methods.R:
76 
+    sgraph
39 77 
 )
40 78
79 
+### Exactly the same list as above.
41 80 
 exportMethods(
42 
-  length,
43 
-  names,
44 
-  elementLengths,
45 
-  Spath,
46 
-  UATXHcount,
47 
-  Sgdf,
48 
-  Sgraph,
49 
-  uninformativeSSids,
50 
-  plot,
51 
-  findOverlaps,
52 
-  encodeOverlaps
81 
+    spath,
82 
+    UATXHcount,
83 
+    sgdf,
84 
+    uninformativeSSids,
85 
+    sgraph
53 86 
 )
87 
+
Browse code

- Define and use the SplicingGraphs S4 container for storing the splicing graphs instead of of a bare GRangesList object. - Replace splicingGraphs() function by SplicingGraphs() constructor. - Make length(), names(), elementLengths(), plot(), findOverlaps(), and encodeOverlaps() work on SplicingGraphs objects by defining appropriate methods. - Replace "Spath" and "UATXHcount" methods for GRangesList objects by methods for SplicingGraphs objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73827 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/02/2013 19:57:05
Showing 1 changed files
NAMESPACE
History View file @ 4f96879
... ... 
@@ -17,6 +17,8 @@ importFrom(Rgraphviz, agopen)
17 17 
 import(GenomicFeatures)
18 18 
 import(Rsamtools)
19 19
20 
+exportClasses(SplicingGraphs)
21 
+
20 22 
 export(
21 23 
   Spath,
22 24 
   UATXHcount,
... ... 
@@ -25,7 +27,7 @@ export(
25 27 
   uninformativeSSids,
26 28 
   Sgdf2,
27 29 
   Sgraph2,
28 
-  splicingGraphs,
30 
+  SplicingGraphs,
29 31
30 32 
   assignSubfeatureHits,
31 33
... ... 
@@ -37,9 +39,15 @@ export(
37 39 
 )
38 40
39 41 
 exportMethods(
42 
+  length,
43 
+  names,
44 
+  elementLengths,
40 45 
   Spath,
41 46 
   UATXHcount,
42 47 
   Sgdf,
43 48 
   Sgraph,
44 
-  uninformativeSSids
49 
+  uninformativeSSids,
50 
+  plot,
51 
+  findOverlaps,
52 
+  encodeOverlaps
45 53 
 )
Browse code

Add toy_overlaps() helper and expand toy_data.Rd man page.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73802 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/02/2013 00:03:48
Showing 1 changed files
NAMESPACE
History View file @ b0d3117
... ... 
@@ -32,6 +32,7 @@ export(
32 32 
   toy_genes_gff,
33 33 
   toy_reads_sam,
34 34 
   toy_reads_bam,
35 
+  toy_overlaps,
35 36 
   plotToyReads
36 37 
 )
37 38
Browse code

Add plotToyReads(), a little helper for plotting toy reads on top of toy genes.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73568 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 15/02/2013 23:23:33
Showing 1 changed files
NAMESPACE
History View file @ e37a000
... ... 
@@ -31,7 +31,8 @@ export(
31 31
32 32 
   toy_genes_gff,
33 33 
   toy_reads_sam,
34 
-  toy_reads_bam
34 
+  toy_reads_bam,
35 
+  plotToyReads
35 36 
 )
36 37
37 38 
 exportMethods(
Browse code

o Replace Sgraph() and Sgraph2() arg 'as.graphNEL' with 'as.Ragraph'. o Remove plotSgraph() and plotSgraph2(). Using plot() instead.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73469 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/02/2013 19:01:10
Showing 1 changed files
NAMESPACE
History View file @ 62d4141
... ... 
@@ -9,8 +9,10 @@ import(BiocGenerics)
9 9 
 import(IRanges)
10 10 
 import(GenomicRanges)
11 11
12 
-import(graph)
13 
-import(Rgraphviz)
12 
+importFrom(graph, nodeDataDefaults, nodeData,
13 
+                  edgeDataDefaults, edgeNames, edgeData)
14 
+
15 
+importFrom(Rgraphviz, agopen)
14 16
15 17 
 import(GenomicFeatures)
16 18 
 import(Rsamtools)
... ... 
@@ -23,7 +25,6 @@ export(
23 25 
   uninformativeSSids,
24 26 
   Sgdf2,
25 27 
   Sgraph2,
26 
-  plotSgraph, plotSgraph2,
27 28 
   splicingGraphs,
28 29
29 30 
   assignSubfeatureHits,
Browse code

depends on graph and Rgraphviz again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73447 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/02/2013 06:21:27
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NAMESPACE
History View file @ 0253d5e
... ... 
@@ -8,6 +8,10 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
8 8 
 import(BiocGenerics)
9 9 
 import(IRanges)
10 10 
 import(GenomicRanges)
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+
12 
+import(graph)
13 
+import(Rgraphviz)
14 
+
11 15 
 import(GenomicFeatures)
12 16 
 import(Rsamtools)
13 17
Browse code

Add assignSubfeatureHits().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73396 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 12/02/2013 01:49:17
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NAMESPACE
History View file @ ca4719b
... ... 
@@ -22,6 +22,8 @@ export(
22 22 
   plotSgraph, plotSgraph2,
23 23 
   splicingGraphs,
24 24
25 
+  assignSubfeatureHits,
26 
+
25 27 
   toy_genes_gff,
26 28 
   toy_reads_sam,
27 29 
   toy_reads_bam
Browse code

Rename UAhc -> UATXHcount (UnAmbiguous Transcript Hit count).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73369 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 11/02/2013 20:13:02
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NAMESPACE
History View file @ 83c547f
... ... 
@@ -13,7 +13,7 @@ import(Rsamtools)
13 13
14 14 
 export(
15 15 
   Spath,
16 
-  UAhc,
16 
+  UATXHcount,
17 17 
   Sgdf,
18 18 
   Sgraph,
19 19 
   uninformativeSSids,
... ... 
@@ -29,7 +29,7 @@ export(
29 29
30 30 
 exportMethods(
31 31 
   Spath,
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-  UAhc,
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+  UATXHcount,
33 33 
   Sgdf,
34 34 
   Sgraph,
35 35 
   uninformativeSSids
Browse code

Complete workflow for unambiguous hit counts.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73299 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/02/2013 23:30:11
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NAMESPACE
History View file @ f4c6c26
... ... 
@@ -13,6 +13,7 @@ import(Rsamtools)
13 13
14 14 
 export(
15 15 
   Spath,
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+  UAhc,
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   Sgdf,
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   Sgraph,
18 19 
   uninformativeSSids,
... ... 
@@ -28,6 +29,7 @@ export(
28 29
29 30 
 exportMethods(
30 31 
   Spath,
32 
+  UAhc,
31 33 
   Sgdf,
32 34 
   Sgraph,
33 35 
   uninformativeSSids
Browse code

Add small SAM file with toy reads.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73277 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/02/2013 03:18:05
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NAMESPACE
History View file @ 7d39f22
... ... 
@@ -19,7 +19,11 @@ export(
19 19 
   Sgdf2,
20 20 
   Sgraph2,
21 21 
   plotSgraph, plotSgraph2,
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-  splicingGraphs
22 
+  splicingGraphs,
23 
+
24 
+  toy_genes_gff,
25 
+  toy_reads_sam,
26 
+  toy_reads_bam
23 27 
 )
24 28
25 29 
 exportMethods(
Browse code

SpliceGraph package reborn as SplicingGraphs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@73245 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/02/2013 21:04:38
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NAMESPACE
History View file @ 50d0360
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,30 @@
1 
+import(methods)
2 
+import(utils)
3 
+
4 
+importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
5 
+                   plot.igraph, igraph.to.graphNEL)
6 
+
7 
+
8 
+import(BiocGenerics)
9 
+import(IRanges)
10 
+import(GenomicRanges)
11 
+import(GenomicFeatures)
12 
+import(Rsamtools)
13 
+
14 
+export(
15 
+  Spath,
16 
+  Sgdf,
17 
+  Sgraph,
18 
+  uninformativeSSids,
19 
+  Sgdf2,
20 
+  Sgraph2,
21 
+  plotSgraph, plotSgraph2,
22 
+  splicingGraphs
23 
+)
24 
+
25 
+exportMethods(
26 
+  Spath,
27 
+  Sgdf,
28 
+  Sgraph,
29 
+  uninformativeSSids
30 
+)