splicingReport {ASpli} | R Documentation |
This function integrates bin and junction usage in a comprehensive report
splicingReport(bdu, jdu, counts)
bdu |
An object of class |
jdu |
An object of class |
counts |
An object of class |
An ASpliSplicingReport
object with junction differential usage report. See vignette for more details
Andres Rabinovich, Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
Accesors: binbased
,
localebased
,
anchorbased
,
Export: writeSplicingReport
gbDUreport
, jDUreport
, ASpliSplicingReport
, splicingReport
# 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)