exportSplicingReports: Export splicing reports

In chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq

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)
  

chernolab/ASpli documentation built on March 11, 2021, 12:24 a.m.