acc_DU: Accessors for ASpliDU object

Description Usage Arguments Value Author(s) Examples

Description

Accessors for ASpliDU object

Usage

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Arguments

x

An ASpliDU object

Value

Returns dataframes with genomic metadata and logFC and pvalue

Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

Examples

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chr14 <- system.file("extdata","chr14.sqlite", package="ASpli")
genome <- loadDb(chr14)
features <- binGenome(genome)
library(RNAseqData.HNRNPC.bam.chr14)
targets <- data.frame(bam=RNAseqData.HNRNPC.bam.chr14_BAMFILES,
                       condition=c(rep("CT",4),rep("KD",4)))
bam <- loadBAM(targets)
counts <- readCounts(features, bam,  l=100L, maxISize=50000);
group <- factor(c(rep("CT",4),rep("KD",4)))
pair <- c("CT","KD")  
du <- DUreport(counts, targets, pair, group)
genesDE(du)
binsDU(du)
junctionsDU(du)


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