parseMisoGeneric {psichomics} | R Documentation

## Parse junctions of an event from MISO according to event type

### Description

Parse junctions of an event from MISO according to event type

### Usage

    parseMisoGeneric(event, validator, eventType, coord, plusIndex, minusIndex)

    parseMisoSE(event)

    parseMisoMXE(event)

    parseMisoRI(event, strand)

    parseMisoA5SS(event)

    parseMisoA3SS(event, plusIndex, minusIndex)

    parseMisoTandemUTR(event, minusIndex)

    parseMisoAFE(event)

    parseMisoALE(event)

### Arguments

`event` | Data.frame containing only one event with at least 7 columns as retrieved from the alternative splicing annotation files from MISO (GFF3 files)
`validator` | Character: valid elements for each event
`eventType` | Character: event type (see details for available events)
`coord` | Character: coordinate positions to fill
`plusIndex` | Integer: index of the coordinates for a plus strand event
`minusIndex` | Integer: index of the coordinates for a minus strand event
`strand` | Character: positive-sense (`+`) or negative-sense `-` strand

### Details

The following event types are available to be parsed:

- SE (exon skipping)

- 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)

- Tandem UTR

### Value

List of parsed junctions

### See Also

`parseMisoEvent()`

### Examples

    # skipped exon event (SE)
    event <- read.table(text = "
      chr1 SE gene 16854 18061 . - .
      chr1 SE mRNA 16854 18061 . - .
      chr1 SE exon 16854 17055 . - .
      chr1 SE exon 17233 17742 . - .
      chr1 SE exon 17915 18061 . - .
      chr1 SE mRNA 16854 18061 . - .
      chr1 SE exon 16854 17955 . - .
      chr1 SE exon 17915 18061 . - .")
    psichomics:::parseMisoSE(event)

    # mutually exclusive exon (MXE) event
    event <- read.table(text = "
     chr1 MXE gene 764383 788090 . + .
     chr1 MXE mRNA 764383 788090 . + .
     chr1 MXE exon 764383 764484 . + .
     chr1 MXE exon 776580 776753 . + .
     chr1 MXE exon 787307 788090 . + .
     chr1 MXE mRNA 764383 788090 . + .
     chr1 MXE exon 764383 764484 . + .
     chr1 MXE exon 783034 783186 . + .
     chr1 MXE exon 787307 788090 . + .")
    psichomics:::parseMisoMXE(event)

    # intron retention (RI) event
    event <- read.table(text = "
     chr1 RI gene 17233 17742 . - .
     chr1 RI mRNA 17233 17742 . - .
     chr1 RI exon 17233 17742 . - .
     chr1 RI mRNA 17233 17742 . - .
     chr1 RI exon 17233 17364 . - .
     chr1 RI exon 17601 17742 . - .")
    psichomics:::parseMisoRI(event)

    # alternative 5' splice site (A5SS) event
    event <- read.table(text = "
     chr1 A5SS gene 17233 17742 . - .
     chr1 A5SS mRNA 17233 17742 . - .
     chr1 A5SS exon 17233 17368 . - .
     chr1 A5SS exon 17526 17742 . - .
     chr1 A5SS mRNA 17233 17742 . - .
     chr1 A5SS exon 17233 17368 . - .
     chr1 A5SS exon 17606 17742 . - .")
    psichomics:::parseMisoA5SS(event)

    # alternative 3' splice site (A3SS) event
    event <- read.table(text = "
     chr1 A3SS gene 15796 16765 . - .
     chr1 A3SS mRNA 15796 16765 . - .
     chr1 A3SS exon 15796 15947 . - .
     chr1 A3SS exon 16607 16765 . - .
     chr1 A3SS mRNA 15796 16765 . - .
     chr1 A3SS exon 15796 15942 . - .
     chr1 A3SS exon 16607 16765 . - .")
    psichomics:::parseMisoA3SS(event)

    # Tandem UTR event
    event <- read.table(text = "
     chr19 TandemUTR gene  10663759  10664625  .  -  .
     chr19 TandemUTR mRNA  10663759  10664625  .  -  .
     chr19 TandemUTR exon  10663759  10664625  .  -  .
     chr19 TandemUTR mRNA  10664223  10664625  .  -  .
     chr19 TandemUTR exon  10664223  10664625  .  -  .")
    psichomics:::parseMisoTandemUTR(event)

    # alternative first exon (AFE) event
    event <- read.table(text = "
     chr12 AFE gene 57916659 57920171  .  +  .
     chr12 AFE mRNA 57919131 57920171  .  +  .
     chr12 AFE exon 57919131 57920171  .  +  .
     chr12 AFE mRNA 57916659 57918199  .  +  .
     chr12 AFE exon 57916659 57916794  .  +  .
     chr12 AFE exon 57917812 57917875  .  +  .
     chr12 AFE exon 57918063 57918199  .  +  .")
    psichomics:::parseMisoAFE(event)

    # alternative last exon (ALE) event
    event <- read.table(text = "
     chr6 ALE gene 30620579 30822593  .  +  .
     chr6 ALE mRNA 30822190 30822593  .  +  .
     chr6 ALE exon 30822190 30822593  .  +  .
     chr6 ALE mRNA 30620579 30620982  .  +  .
     chr6 ALE exon 30620579 30620982  .  +  .")
    psichomics:::parseMisoALE(event)

[Package psichomics version 1.12.1 Index]