exportSplicingReports {ASpli} | R Documentation |
Export splicing reports in easy to analyze HTML tables.
exportSplicingReports( sr, output.dir="sr" , openInBrowser = FALSE, maxBinFDR = 0.2, maxJunctionFDR = 0.2 )
sr |
An object of class |
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 |
Produces html reports
Andres Rabinovich, Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
gbDUreport
, jDUreport
, splicingReport
, ASpliSplicingReport
# 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)