Accessors for ASpliAS object

Share:

Description

Accessors for ASpliAS object

Usage

1
2
3
4
5
6

Arguments

x

An ASpliAS object

Value

Returns dataframes with genomic metadata and PSI and PIR metrics

Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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")  
as <- AsDiscover(counts, targets, features, bam, threshold=5, l=100, pair=pair)
altPSI(as)
esPSI(as)
irPIR(as)
joint(as)
junctionsPIR(as)
junctionsPSI(as)