AsDiscover-methods: Report PSI and PIR using experimental junctions

Description Usage Arguments Value Author(s) See Also Examples

Description

Given a bin, it is possible to calculate PSI/PIR metric using junctions to estimate changes in the use of it along different conditions.

Usage

1
2
3
4
5
6
7
8
AsDiscover(counts, 
          targets, 
          features, 
          bam, 
          l,
          pair,
          threshold, 
          cores)

Arguments

counts

An object of class ASpliCounts.

targets

A dataframe containing sample, bam and condition columns

features

An object of class ASpliFeatures.

bam

A list with BAM files

l

Read length of sequenced read. Default 100L

pair

Vector of length two, either numeric or character, providing the pair of groups to be compared

threshold

Minimun number of reads supporting junctions. Default=5

cores

Number of proccesors to use

Value

An object of class ASpliAS

irPIR

reports: event, e1i counts (J1), ie1 counts (J2), j_within (J3), PIR by condition. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.

altPSI

reports: event, J1 (start), J2 (end), J3 (exclusion), PSI. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.

esPSI

reports: event, J1 (start), J2 (end), J3 (exclusion), PSI. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.

junctionsPIR

PIR metric for each experimental junction using e1i and ie2 counts. Exclusion junction is the junction itself. This output helps to discover new introns as well as new retention events

junctionsPSI

Given a junction, it is possible to analyze if it shares start, end or both with another junction. If so, is because there is more than one way for/of splicing. Using strand information it is possible to classify those pair of junctions into Alt5'ss, Alt3'ss or ES. Ratio between them along samples is reported.

Author(s)

Estefania Mancini, Marcelo Yanovsky and Ariel Chernomoretz

See Also

Accesors: irPIR, altPSI, esPSI, junctionsPIR,junctionsPSI Export: writeAS

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
library(RNAseqData.HNRNPC.bam.chr14)
chr14 <- system.file("extdata","chr14.sqlite", package="ASpli")
genome <- loadDb(chr14)
features <- binGenome(genome)
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, l=100L, pair=pair)
writeAS(as=as, output.dir="only_as")

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