splicingReport {ASpli} | R Documentation

## Splicing report

### Description

This function integrates bin and junction usage in a comprehensive report

### Usage

      splicingReport(bdu, jdu, counts)

### Arguments

`bdu` | An object of class `ASpliDU`
`jdu` | An object of class `ASpliJDU`
`counts` | An object of class `ASpliCounts`

### Value

An `ASpliSplicingReport` object with junction differential usage report. See vignette for more details

### Author(s)

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

### See Also

Accesors: `binbased`, `localebased`, `anchorbased`, Export: `writeSplicingReport` `gbDUreport`, `jDUreport`, `ASpliSplicingReport`, `splicingReport`

### 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)

    # Access splicing report elements
    sr
    localebased(sr)
    anchorbased(sr)
    binbased(sr)

[Package ASpli version 2.0.0 Index]