quantifyPSI {ASpediaFI} | R Documentation

## AS event quantification

### Description

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

### Usage

    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

    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)

[Package ASpediaFI version 1.2.0 Index]