exportSplicingReports {ASpli} | R Documentation

## Export splicing reports

### Description

Export splicing reports in easy to analyze HTML tables.

### Usage

    exportSplicingReports( sr, output.dir="sr" ,
    openInBrowser = FALSE, maxBinFDR = 0.2, maxJunctionFDR = 0.2 )

### Arguments

`sr` | An object of class `ASpliSplicingReport`
`output.dir` | HTML reports output directory
`openInBrowser` | Open reports in browser when done
`maxBinFDR` | Only show bins with FDR < maxBinFDR
`maxJunctionFDR` | Only show junctions with FDR < maxJunctionFDR

### Value

Produces html reports

### Author(s)

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

### See Also

`gbDUreport`, `jDUreport`, `splicingReport`, `ASpliSplicingReport`

### 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)

      # Export splicing report
      exportSplicingReports(output.dir = paste0(tempdir(), "/sr"), sr)

[Package ASpli version 2.0.0 Index]