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 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 in different ways.

Details

See the Splicing graphs and RNA-seq data vignette in the package for a gentle introduction to its use. To access the vignette, do browseVignettes("SplicingGraphs"), then click on the link to the PDF version.

Note

The SplicingGraphs package is a reincarnation of an internal project, the SpliceGraph package, originally written by D. Bindreither, M. Carlson, and M. Morgan. SpliceGraph was never released as part of Bioconductor.

With respect to the old SpliceGraph, the scope of the new SplicingGraphs package has been reduced to focus only on the following functionalities: creating/manipulating/plotting splicing graphs, computing the bubbles and AS codes, and assigning/counting reads.

In addition to this, the old SpliceGraph package also had facilities for performing some downstream statistical analysis. They were covered in its vignette under the following topics/sections:

• Experimental design

• Significant altered alternative splice events

• Modification of GLM employed in the DEXSeq package

• Differential edge expression analysis

• Comparison to the classic DEXSeq analysis

The SplicingGraphs vignette doesn't cover any of this and the new package provides no facilities for doing this type of downstream statistical analysis.

Author(s)

Author and maintainer: H. Pages <hpages@fredhutch.org>

The SplicingGraphs package is a complete revamp (design and implementation) of the old SpliceGraph package (see Note above).

References

Heber, S., Alekseyev, M., Sze, S., Tang, H., and Pevzner, P. A. Splicing graphs and EST assembly problem Bioinformatics Date: Jul 2002 Vol: 18 Pages: S181-S188

Sammeth, M. (2009) Complete Alternative Splicing Events Are Bubbles in Splicing Graphs J. Comput. Biol. Date: Aug 2009 Vol: 16 Pages: 1117-1140

See Also

The man pages in the SplicingGraphs package are:

1. The SplicingGraphs class.

2. plotTranscripts for plotting a set of transcripts along genomic coordinates.

3. sgedgesByGene for extracting the edges and their ranges from a SplicingGraphs object.

4. txpath for extracting the transcript paths of a splicing graph.

5. sgedges for extracting the edges (and nodes) of a splicing graph.

6. sgraph for extracting a splicing graph as a plottable graph-like object.

7. rsgedgesByGene for extracting the reduced edges and their ranges from a SplicingGraphs object.

8. bubbles for computing the bubbles of a splicing graph.

9. assignReads for assigning reads to the edges of a SplicingGraphs object.

10. countReads for summarizing the reads assigned to a SplicingGraphs object.

11. toy_genes_gff for details about the toy data included in this package.

Examples

if (interactive()) {
  ## Access the "Splicing graphs and RNA-seq data" vignette with:
  browseVignettes("SplicingGraphs")
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SplicingGraphs)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:Biostrings':

    complement

Loading required package: grid

Attaching package: 'Rgraphviz'

The following objects are masked from 'package:IRanges':

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs' 
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SplicingGraphs/SplicingGraphs-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SplicingGraphs-package
> ### Title: Create, manipulate, visualize splicing graphs, and assign
> ###   RNA-seq reads to them
> ### Aliases: SplicingGraphs-package
> ### Keywords: package
> 
> ### ** Examples
> 
> #if (interactive()) {
>   ## Access the "Splicing graphs and RNA-seq data" vignette with:
>   browseVignettes("SplicingGraphs")
starting httpd help server ... done
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>