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 )

[Package ASpli version 2.0.0 Index]