parseMisoGeneric: Parse junctions of an event from MISO according to event type

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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 (retained intron)

• 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)

# retained intron (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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.