exportIntegratedSignals {ASpli} | R Documentation |
Export integrated signals in an easy to analyze HTML table.
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 )
is |
An object of class |
sr |
An object of class |
counts |
An object of class |
features |
An object of class |
asd |
An object of class |
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 |
Produces html reports
Andres Rabinovich, Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
gbDUreport
, jDUreport
, ASpliSplicingReport
, splicingReport
, \
codeASpliIntegratedSignals
# 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 )