splicingReport: Splicing report

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

Description

This function integrates bin and junction usage in a comprehensive report

Usage

  splicingReport(bdu, jdu, counts)

Arguments

bdu	An object of class ASpliDU
jdu	An object of class ASpliJDU
counts	An object of class ASpliCounts

Value

An ASpliSplicingReport object with junction differential usage report. See vignette for more details

Author(s)

Andres Rabinovich, Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

See Also

Accesors: binbased, localebased, anchorbased, Export: writeSplicingReport gbDUreport, jDUreport, ASpliSplicingReport, splicingReport

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)

# Access splicing report elements
sr  
localebased(sr)
anchorbased(sr)
binbased(sr)

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