integrateSignals {ASpli} | R Documentation |
Integrates differential usage signals from different sources using overlaping regions. See vignette for more details
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")
sr |
An object of class |
asd |
An object of class |
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". |
It returns A ASpliIntegratedSignals
with all overlaping signals present in the region filtered by different parameters.
Andres Rabinovich, Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
Accesors: signals,
filters,
Export: exportIntegratedSignals
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'), 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)