parseSuppaGeneric {psichomics} | R Documentation

## Parse junctions of an event from SUPPA

### Description

Parse junctions of an event from SUPPA

### Usage

    parseSuppaGeneric(junctions, strand, coords, plus_pos, minus_pos)

    parseSuppaSE(junctions, strand)

    parseSuppaRI(junctions, strand)

    parseSuppaALE(junctions, strand)

    parseSuppaAFE(junctions, strand)

    parseSuppaMXE(junctions, strand)

    parseSuppaA3SS(junctions, strand)

    parseSuppaA5SS(junctions, strand)

### Arguments

`junctions` | List of integers: exon-exon junctions of an event
`strand` | Character: positive-sense (`+`) or negative-sense (`-`) strand
`coords` | Character: coordinate positions to fill
`plus_pos` | Integer: index of the coordinates for a plus strand event
`minus_pos` | Integer: index of the coordinates for a minus strand event

### Details

The following event types are available to be parsed:

- SE (exon skipping)

- RI (intron retention)

- MXE (mutually exclusive exons)

- A5SS (alternative 5' splice site)

- A3SS (alternative 3' splice site)

- ALE (alternative last exon)

- AFE (alternative first exon)

### Value

Data frame of parsed junctions

### See Also

`parseSuppaEvent()`

### Examples

    # Parse generic event (in this case, an exon skipping event)
    junctions <- read.table(text = "169768099 169770024 169770112 169771762")
    coords <- c("C1.end", "A1.start", "A1.end", "C2.start")
    plus  <- 1:4
    minus <- 1:4
    psichomics:::parseSuppaGeneric(junctions, strand = "+", coords, plus, minus)

    junctions <- read.table(text = "169768099 169770024 169770112 169771762")
    psichomics:::parseSuppaSE(junctions, "+")

    junctions <- read.table(text = "196709749 196709922 196711005 196711181")
    psichomics:::parseSuppaRI(junctions, "+")

    junctions <- read.table(
        text = "24790610 24792494 24792800 24790610 24795476 24795797")
    psichomics:::parseSuppaALE(junctions, "+")

    junctions <- read.table(
        text = "169763871 169764046 169767998 169764550 169765124 169767998")
    psichomics:::parseSuppaAFE(junctions, "+")

    junctions <- read.table(
        text = "202060671 202068453 202068489 202073793 202060671 202072798 202072906 202073793")
    psichomics:::parseSuppaMXE(junctions, "+")

    junctions <- read.table(text = "169772450 169773216 169772450 169773253")
    psichomics:::parseSuppaA3SS(junctions, "+")

    junctions <- read.table(text = "50193276 50197008 50192997 50197008")
    psichomics:::parseSuppaA5SS(junctions, "+")

[Package psichomics version 1.14.1 Index]