integrateSignals: Integrate signals
In chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description Usage Arguments Value Author(s) See Also Examples

Integrates differential usage signals from different sources using overlaping regions. See vignette for more details

  integrateSignals(sr = NULL, asd = NULL, bin.FC = 3, bin.fdr = 0.05,
                 nonunif = 1, usenonunif = FALSE, bin.inclussion = 0.2,
                 bjs.inclussion = 10.3, bjs.fdr = 0.01, a.inclussion =
                 0.3, a.fdr = 0.01, l.inclussion = 0.3, l.fdr = 0.01,
                 otherSources = NULL, overlapType = "any")

`sr`	An object of class `ASpliSplicingReport`
`asd`	An object of class `ASpliDU`
`bin.FC`	Filter bin signals by fold change. Actually, log2 fold change is return, so default would return only bin signlas with bin.fc > log2(3).
`bin.fdr`	Filter bin signals by fdr.
`nonunif`	Filter intronic bins with non uniform support (nonunif << 1 is uniform)
`usenonunif`	Use non uniformity as filter.
`bin.inclussion`	Filter bin signals by junction support with dPIR or dPSI accordingly.
`bjs.inclussion`	Filter annotated junction signals by junction inclussion with dPIR or dPSI accordingly.
`bjs.fdr`	Filter annotated junction signals by fdr.
`a.inclussion`	Filter anchor junction signals by junction inclussion with dPIR.
`a.fdr`	Filter anchor junction signals by fdr.
`l.inclussion`	Filter locale junction signals by junction inclussion with dPSI.
`l.fdr`	Filter locale junction signals by fdr.
`otherSources`	If user wants to compare ASpli results with results from other methods, otherSources must be a GenomicRange object with all the regions found with the other methods. It will be integrated with a new column next to signals information.
`overlapType`	Type of regions overlap matching between the different signals. Defaults to "any" and can be any of the following: "any", "start", "end", "within", "equal".

It returns A ASpliIntegratedSignals with all overlaping signals present in the region filtered by different parameters.

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

Accesors: signals, filters, Export: exportIntegratedSignals gbDUreport, jDUreport, ASpliSplicingReport, splicingReport, \ codeASpliIntegratedSignals

  # Create a transcript DB from gff/gtf annotation file.
  # Warnings in this examples can be ignored. 
  library(GenomicFeatures)
  genomeTxDb <- makeTxDbFromGFF( system.file('extdata','genes.mini.gtf', 
                                 package="ASpli") )
  
  # Create an ASpliFeatures object from TxDb
  features <- binGenome( genomeTxDb )
  
  # Define bam files, sample names and experimental factors for targets.
  bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", 
                     "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )

  targets <- data.frame( 
               row.names = paste0('Sample_',c(1:6)),
               bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
               factor1 = c( 'C','C','C','D','D','D'),
               subject = c(0, 1, 2, 0, 1, 2))
  
  # Read counts from bam files
gbcounts  <- gbCounts( features = features, 
                           targets = targets, 
                           minReadLength = 100, maxISize = 50000,
                           libType="SE", 
                           strandMode=0)
jcounts   <- jCounts(counts = gbcounts, 
                     features = features, 
                     minReadLength = 100,
                     libType="SE", 
                     strandMode=0)
                     

  # Test for factor1 controlling for paired subject
  gbPaired <- gbDUreport(gbcounts, formula = formula(~subject+factor1))
  jPaired  <- jDUreport(jcounts, formula = formula(~subject+factor1))
  
  # Generate a splicing report merging bins and junctions DU
  sr       <- splicingReport(gbPaired, jPaired, gbcounts)
  is       <- integrateSignals(sr, jcounts)
  
  # Show integrate signals results and filters used
  signals(is)
  filters(is)