exportIntegratedSignals {ASpli}

R Documentation

Export integrated signals.

Description

Export integrated signals in an easy to analyze HTML table.

Usage

exportIntegratedSignals( is, output.dir="is", 
                         sr, counts, features, asd,
                         mergedBams, 
                         jCompletelyIncluded = FALSE, zoomRegion = 1.5, 
                         useLog = FALSE, tcex = 1, ntop = NULL, 
                         openInBrowser = FALSE, 
                         makeGraphs = TRUE, bforce=FALSE
                        )

Arguments

is	An object of class ASpliIntegratedSignals
sr	An object of class ASpliSplicingReport
counts	An object of class ASpliCounts
features	An object of class ASpliFeatures
asd	An object of class ASpliAS
output.dir	HTML reports output directory
mergedBams	Dataframe with two columns, bams and conditions. Bams are paths to merged bams for each condition to be ploted.
jCompletelyIncluded	If TRUE only plot junctions completely included in plot region. Else plot any overlapping junction in the region
zoomRegion	Magnify plot region by this factor
useLog	Plot counts log
tcex	Text size
ntop	Only show n top signals
openInBrowser	Open reports in browser when done
makeGraphs	Generate graphs in reports
bforce	Force plot generation even if plot already exists

Value

Produces html reports

Author(s)

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

See Also

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'))
  
  # 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
  gbPaired <- gbDUreport(gbcounts, contrast = c(1, -1))
  jPaired  <- jDUreport(jcounts, , contrast = c(1, -1))
  
  # Generate a splicing report merging bins and junctions DU
  sr       <- splicingReport(gbPaired, jPaired, gbcounts)
  is       <- integrateSignals(sr, jcounts)
  
  #Make merged bams dataframe
  mergedBamsFileNames <- c( "A_C.bam", "A_D.bam" )
  mergedBams <- data.frame(bams = system.file( 'extdata', mergedBamsFileNames, package="ASpli" ), 
  condition = c("C", "D"), stringsAsFactors = FALSE)
  
  # Export integrated signals
  exportIntegratedSignals(is, output.dir = paste0(tempdir(), "/is"), sr, gbcounts,
                        features, jcounts, mergedBams, makeGraphs = TRUE, bforce = TRUE )
  

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