Examine ASpliDU objects {ASpli} | R Documentation

## Examine ASpliDU objects

### Description

AspliDU object may contain results of differential expression of genes, differential usage of bins and junctions, however not everything is calculated at the same or even present. Calculations for genes and bins can be done independently from junctions. Functions `containsJunctions` and `containsGenesAndBins` allow to interrogate an ASpliDU object about the kind of results it contain.

### Usage

      containsJunctions( du )
      containsGenesAndBins( du )

### Arguments

`du` | An ASpliDU object.

### Value

A logical value that indicates that results for genes and bins, or results for junctions are available in the object.

### Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

### 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') )

      # Load reads from bam files
      bams <- loadBAM( targets )

      # Read counts from bam files
      counts   <- readCounts( features, bams, targets, cores = 1, readLength = 100,
                              maxISize = 50000 )

      # Create an ASpliDU object.
      #
      du       <- DUreport( counts, targets )

      # Verify if du contains results for genes and bins.
      containsGenesAndBins( du )
      containsJunctions( du )

      # Append junction results
      du       <- junctionDUreport( counts, targets, appendTo = du )

      # Verify if du contains results for genes and bins.
      containsJunctions( du )

[Package ASpli version 1.14.0 Index]