integrateSignals: Integrate signals

In ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description

Integrates differential usage signals from different sources using overlaping regions. See vignette for more details

Usage

  integrateSignals(sr = NULL, asd = NULL, bin.FC = 3, bin.fdr = 0.05,
                 nonunif = 1, usenonunif = FALSE, bin.inclussion = 0.2,
                 bjs.inclussion = 10.3, bjs.fdr = 0.01, a.inclussion =
                 0.3, a.fdr = 0.01, l.inclussion = 0.3, l.fdr = 0.01,
                 otherSources = NULL, overlapType = "any")

Arguments

sr	An object of class ASpliSplicingReport
asd	An object of class ASpliDU
bin.FC	Filter bin signals by fold change. Actually, log2 fold change is return, so default would return only bin signlas with bin.fc > log2(3).
bin.fdr	Filter bin signals by fdr.
nonunif	Filter intronic bins with non uniform support (nonunif << 1 is uniform)
usenonunif	Use non uniformity as filter.
bin.inclussion	Filter bin signals by junction support with dPIR or dPSI accordingly.
bjs.inclussion	Filter annotated junction signals by junction inclussion with dPIR or dPSI accordingly.
bjs.fdr	Filter annotated junction signals by fdr.
a.inclussion	Filter anchor junction signals by junction inclussion with dPIR.
a.fdr	Filter anchor junction signals by fdr.
l.inclussion	Filter locale junction signals by junction inclussion with dPSI.
l.fdr	Filter locale junction signals by fdr.
otherSources	If user wants to compare ASpli results with results from other methods, otherSources must be a GenomicRange object with all the regions found with the other methods. It will be integrated with a new column next to signals information.
overlapType	Type of regions overlap matching between the different signals. Defaults to "any" and can be any of the following: "any", "start", "end", "within", "equal".

Value

It returns A ASpliIntegratedSignals with all overlaping signals present in the region filtered by different parameters.

Author(s)

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

See Also

Accesors: signals, filters, Export: exportIntegratedSignals gbDUreport, jDUreport, ASpliSplicingReport, splicingReport, \ codeASpliIntegratedSignals

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)
  is       <- integrateSignals(sr, jcounts)
  
  # Show integrate signals results and filters used
  signals(is)
  filters(is)

ASpli documentation built on Nov. 8, 2020, 5:21 p.m.