Examine ASpliDU objects {ASpli} | R Documentation |
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.
containsJunctions( du ) containsGenesAndBins( du )
du |
An ASpliDU object. |
A logical value that indicates that results for genes and bins, or results for junctions are available in the object.
Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz
# 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 )