ASpli-package: Analysis of Alternative Splicing Using RNAseq

Description Details Author(s) References Examples

Description

ASpli is an integrative and flexible package that facilitates the characterization of genome-wide changes in AS under different experimental conditions. ASpli analyzes the differential usage of introns, exons, and splice junctions using read counts, and estimates the magnitude of changes in AS by calculating differences in the percentage of exon inclusion or intron retention using splice junctions. This integrative approach allows the identification of changes in both annotated and novel AS events.

ASpli allows users to produce self-explanatory intermediate outputs, based on the aim of their analysis. A typical workflow involves parsing the genome annotation into new features called bins, overlapping read alignments against those bins, and inferring differential bin usage based on the number of reads aligning to the bins and junctions.

Details

Package: ASpli
Type: Package
Version: 1.5.1
Date: 2018-02-22
License: GPL
Depends: methods, GenomicRanges, GenomicFeatures, edgeR, methods, BiocGenerics, IRanges, GenomicAlignments, Gviz

Author(s)

Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

References

Examples

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library(GenomicFeatures)
gtfFileName <- aspliExampleGTF()
genomeTxDb <- makeTxDbFromGFF( gtfFileName )
features <- binGenome( genomeTxDb )
BAMFiles <- aspliExampleBamList()
targets <- data.frame( 
  row.names = paste0('Sample',c(1:12)),
  bam = BAMFiles,
  f1 = c( 'A','A','A','A','A','A',
          'B','B','B','B','B','B'),
  f2 = c( 'C','C','C','D','D','D',
          'C','C','C','D','D','D'),
  stringsAsFactors = FALSE)
  getConditions(targets)
  mBAMs <- data.frame(bam      = sub("_[02]","",targets$bam[c(1,4,7,10)]),
                      condition= c("A_C","A_D","B_C","B_D"))

gbcounts  <- gbCounts( features = features, 
                           targets = targets, 
                           minReadLength = 100, maxISize = 50000,
                           libType="SE", 
                           strandMode=0)
asd   <- jCounts(counts = gbcounts, 
                     features = features, 
                     minReadLength = 100,
                     libType="SE", 
                     strandMode=0)
                     
   
gb      <- gbDUreport(counts=gbcounts,
contrast = c( 1, -1, -1, 1 ) )
jdur    <- jDUreport(asd, 
                     contrast =  c( 1, -1, -1, 1 ) ,
                     mergedBams = mBAMs)
sr      <- splicingReport(gb, jdur, counts =gbcounts    )
is      <- integrateSignals(sr,asd)

ASpli documentation built on Nov. 8, 2020, 5:21 p.m.