quantifyPSI: AS event quantification

Description Usage Arguments Value References Examples

View source: R/quantifyPSI.R

Description

Compute PSI values of AS events. This function borrows code from the IMAS package.

Usage

1
2
quantifyPSI(object, read.type = "paired", read.length, insert.size,
    min.reads, num.cores = 1)

Arguments

object

Object of class ASpediaFI

read.type

a type of RNA-seq reads ('single' or 'paired')

read.length

read length

insert.size

insert size

min.reads

a minimum number of reads mapped to a given exon

num.cores

the number of cores for parallel processing

Value

ASpediaFI object with PSI values

References

Han, S. et al. (2017). IMAS: Integrative analysis of Multi-omics data for Alternative Splicing. R package version 1.8.0.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
bamWT <- system.file('extdata/GSM3167290.subset.bam', package = 'ASpediaFI')
GSE114922.ASpediaFI <- ASpediaFI(
    sample.names = 'GSM3167290',
    bam.files = bamWT, conditions = 'WT'
)
## Not run: 
GSE114922.ASpediaFI <- quantifyPSI(GSE114922.ASpediaFI,
    read.type = 'paired',
    read.length = 100, insert.size = 300,
    min.reads = 3, num.cores = 1
)

## End(Not run)

nachoryu/ASpediaFI documentation built on April 6, 2020, 10:49 a.m.