exportIntegratedSignals: Export integrated signals.

Description Usage Arguments Value Author(s) See Also Examples

Description

Export integrated signals in an easy to analyze HTML table.

Usage

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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

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  # 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 )
  

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