parseVastToolsSE {psichomics} | R Documentation

## Parse junctions of an event from VAST-TOOLS according to event type

### Description

Parse junctions of an event from VAST-TOOLS according to event type

### Usage

    parseVastToolsSE(junctions)

    parseVastToolsRI(junctions, strand)

    parseVastToolsA3SS(junctions)

    parseVastToolsA5SS(junctions)

### Arguments

`junctions` | Data.frame or matrix: exon-exon junctions of alternative splicing events (it must have 4 columns)
`strand` | Character: positive (+) or negative (-) strand

### Details

The following event types are available to be parsed:

- SE (skipped exon)

- RI (intron retention)

- A5SS (alternative 5' splice site)

- A3SS (alternative 3' splice site)

### Value

List of parsed junctions

### See Also

`parseVastToolsEvent()`

### Examples

    junctions <- read.table(text = "41040823 41046768 41046903 41051785")
    psichomics:::parseVastToolsSE(junctions)

    # these functions are vectorised!
    junctions <- read.table(text = "41040823 41046768 41046903 41051785
                                    58864658 58864693 58864294 58864563")
    psichomics:::parseVastToolsSE(junctions)

    junctions <- read.table(text = "58864658 58864693 58864294 58864563")
    psichomics:::parseVastToolsRI(junctions, strand = "+")

    junctions <- rbind(
        c(36276385, list(c(36277798, 36277315)), 36277974),
        c(7133604, 7133377, list(c(7133474, 7133456)))
    )
    psichomics:::parseVastToolsA3SS(junctions)

    junctions <- rbind(
        c(74650610, list(c(74650654, 74650658)), 74650982),
        c(list(c(49557666, 49557642), 49557746, 49557470))
    )
    psichomics:::parseVastToolsA5SS(junctions)

[Package psichomics version 1.12.1 Index]