quantifySplicing {psichomics} | R Documentation

## Quantify alternative splicing events

### Description

Quantify alternative splicing events

### Usage

    quantifySplicing(annotation, junctionQuant, eventType = c("SE", "MXE",
      "ALE", "AFE", "A3SS", "A5SS"), minReads = 10, genes = NULL)

### Arguments

`annotation` | List of data frames: annotation for each alternative splicing event type
`junctionQuant` | Data frame: junction quantification
`eventType` | Character: splicing event types to quantify
`minReads` | Integer: discard alternative splicing quantified using a number of reads below this threshold
`genes` | Character: gene symbols for which the splicing quantification of associated splicing events is performed (by default, all splicing events undergo splicing quantification)

### Value

Data frame with the quantification of the alternative splicing events

### Examples

    # Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events
    annot <- readFile("ex_splicing_annotation.RDS")
    junctionQuant <- readFile("ex_junctionQuant.RDS")

    psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))

[Package psichomics version 1.8.2 Index]