integrateSignals {ASpli} | R Documentation

## Integrate signals

### Description

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

### Usage

      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")

### Arguments

`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".

### Value

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

### Author(s)

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

### See Also

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

### Examples

      # 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)

[Package ASpli version 2.4.0 Index]