acc_counts: Accessors for ASpliCounts object

In estepi/ASpli: Analysis of alternative splicing using RNA-Seq

Description

Accessors for ASpliCounts object

Usage

countsb(x)
countse1i(x)
countsg(x)
countsie2(x)
countsj(x)
rdsg(x)
rdsb(x)

Arguments

x	An ASpliCounts object

Value

Returns dataframes with counts by sample and genomic metadata

Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

Examples

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);
countsb(counts)
countse1i(counts)
countsg(counts)
countsie2(counts)
countsj(counts)
rdsg(counts)
rdsb(counts)

estepi/ASpli documentation built on May 16, 2019, 8:53 a.m.