50d0360b |
import(methods)
import(utils)
importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,
plot.igraph, igraph.to.graphNEL)
import(BiocGenerics)
|
ab342602 |
import(S4Vectors)
|
50d0360b |
import(IRanges)
|
00ea746d |
import(GenomeInfoDb)
|
50d0360b |
import(GenomicRanges)
|
b129389b |
import(GenomicFeatures)
|
1d57ccfd |
importFrom(Rsamtools, asBam)
|
05644e55 |
import(GenomicAlignments)
|
0253d5e4 |
|
62d41418 |
importFrom(graph, nodeDataDefaults, nodeData,
|
00ea746d |
edgeDataDefaults, edgeNames, edgeData, edgemode)
|
62d41418 |
|
00ea746d |
importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)
|
0253d5e4 |
|
a48698ec |
exportClasses(GeneModel, SplicingGraphs)
|
4f96879b |
|
5712a4d7 |
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in SplicingGraphs
###
exportMethods(
|
69a8543c |
length,
names,
|
48887b0e |
show,
|
69a8543c |
"[",
"[[",
elementLengths,
unlist,
|
937fc96c |
seqnames,
strand,
|
66886f49 |
seqinfo,
|
dd0bd6a7 |
intronsByTranscript,
|
77742862 |
plot
|
5712a4d7 |
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
24537e93 |
### Export non-generic functions (and non-function symbols)
|
5712a4d7 |
###
export(
## sgraph-methods.R:
|
e4018036 |
slideshow,
|
5712a4d7 |
|
9ce7e847 |
## rsgedgesByGene-methods.R:
rsgedges, sgedges2,
rsgraph, sgraph2,
|
24537e93 |
## bubbles-methods.R:
ASCODE2DESC,
|
75d6518f |
## assignReads.R:
|
1701fd0c |
assignReads,
|
650ba9d1 |
removeReads,
|
5712a4d7 |
## toy_data.R:
toy_genes_gff,
toy_reads_sam,
toy_reads_bam,
|
2c9e1ed4 |
toy_overlaps
|
5712a4d7 |
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in SplicingGraphs + export corresponding
### methods
###
|
50d0360b |
export(
|
cb383bfe |
## SplicingGraphs-class.R:
SplicingGraphs,
|
d52043c4 |
## plotTranscripts-methods.R:
plotTranscripts,
|
942a5908 |
## sgedgesByGene-methods.R:
|
6c1f4100 |
sgedgesByTranscript,
|
9cd225cb |
sgedgesByGene,
|
6c1f4100 |
|
7ff5c4a7 |
## txpath-methods.R:
txpath,
|
475e1010 |
txweight, "txweight<-",
|
7ff5c4a7 |
## sgedges-methods.R:
|
b72ecced |
sgedges,
|
f3bb380b |
sgnodes,
|
aaaabdf7 |
outdeg, indeg,
|
5712a4d7 |
## sgraph-methods.R:
|
261b4730 |
sgraph,
|
43e1ae98 |
## rsgedgesByGene-methods.R:
|
0861db8a |
uninformativeSSids,
|
43e1ae98 |
rsgedgesByTranscript,
|
c10df4de |
rsgedgesByGene,
|
9ce7e847 |
## bubbles-methods.R:
bubbles,
|
c10df4de |
|
94444bda |
## countReads-methods.R:
|
189b61d3 |
reportReads,
|
c10df4de |
countReads
|
50d0360b |
)
|
5712a4d7 |
### Exactly the same list as above.
|
50d0360b |
exportMethods(
|
cb383bfe |
SplicingGraphs,
|
d52043c4 |
plotTranscripts,
|
6c1f4100 |
sgedgesByTranscript,
|
9cd225cb |
sgedgesByGene,
|
7ff5c4a7 |
txpath,
|
475e1010 |
txweight, "txweight<-",
|
b72ecced |
sgedges,
|
f3bb380b |
sgnodes,
|
aaaabdf7 |
outdeg, indeg,
|
261b4730 |
sgraph,
|
9ce7e847 |
uninformativeSSids,
|
43e1ae98 |
rsgedgesByTranscript,
|
c10df4de |
rsgedgesByGene,
|
9ce7e847 |
bubbles,
|
189b61d3 |
reportReads,
|
c10df4de |
countReads
|
50d0360b |
)
|
5712a4d7 |
|