parseMatsGeneric {psichomics} | R Documentation

## Parse junctions of an alternative splicing event from MATS according to event type

### Description

Parse junctions of an alternative splicing event from MATS according to event type

### Usage

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

    parseMatsSE(junctions, strand)

    parseMatsMXE(junctions, strand)

    parseMatsRI(junctions, strand)

    parseMatsA3SS(junctions, strand)

    parseMatsA5SS(junctions, strand)

    parseMatsAFE(junctions, strand)

    parseMatsALE(junctions, strand)

### Arguments

`junctions` | Integer: event's junctions
`strand` | Character: strand of the event
`coords` | Character: names of the alternative splicing coordinates
`plus_pos` | Integer: match of each junction in the respective coordinate for the plus strand
`minus_pos` | Integer: match of each junction in the respective coordinate for the minus strand

### Details

The following event types are ready to be parsed:

- SE (skipped exon)

- MXE (mutually exclusive exon)

- RI (intron retention)

- A5SS (alternative 5' splice site)

- A3SS (alternative 3' splice site)

- AFE (alternative first exon)

- ALE (alternative last exon)

You can use `parseMatsGeneric` to parse other event types.

### Value

Data frame with parsed junctions

### See Also

`parseMatsEvent`

### Examples

    # Parse generic event (in this case, an exon skipping event)
    junctions <- read.table(text=
        "79685787 79685910 79685796 79685910 79679566 79679751")
    coords <- c("A1.start", "A1.end",
                "C1.start", "C1.end",
                "C2.start", "C2.end")
    plus  <- c(1:6)
    minus <- c(2:1, 6:3)
    psichomics:::parseMatsGeneric(junctions, strand = "+", coords, plus, minus)

    # Parse exon skipping event
    junctions <- read.table(text=
        "79685787 79685910 79685796 79685910 79679566 79679751")
    psichomics:::parseMatsSE(junctions, strand = "+")

    # Parse mutually exclusive exon event
    junctions <- read.table(text=
    "158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199")
    psichomics:::parseMatsMXE(junctions, strand = "+")

    # Parse intron retention event
    junctions <- read.table(text=
        "15929853 15932100 15929853 15930016 15930687 15932100")
    psichomics:::parseMatsRI(junctions, strand = "+")

    # Parse alternative 3' splicing site event
    junctions <- read.table(text=
        "79685787 79685910 79685796 79685910 79679566 79679751")
    psichomics:::parseMatsA3SS(junctions, strand = "+")

    # Parse alternative 5' splicing site event
    junctions <- read.table(text=
        "102884421 102884501 102884421 102884489 102884812 102885881")
    psichomics:::parseMatsA5SS(junctions, strand = "+")

    # Parse alternative first exon event
    junctions <- read.table(text=
        "16308723 16308879 16308967 16309119 16314269 16314426")
    psichomics:::parseMatsAFE(junctions, strand = "+")

    # Parse alternative last exon event
    junctions <- read.table(text=
        "111858645 111858828 111851063 111851921 111850441 111850543")
    psichomics:::parseMatsAFE(junctions, strand = "+")

[Package psichomics version 1.8.2 Index]