getValidEvents {psichomics} | R Documentation

## Filters the events with valid elements according to the given validator

### Description

Filters the events with valid elements according to the given validator

### Usage

    getValidEvents(event, validator, areMultipleExonsValid = FALSE)

### 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
`areMultipleExonsValid` | Boolean: consider runs of exons as valid when comparing with the validator? Default is FALSE (see details)

### Details

`areMultipleExonsValid` allows to consider runs of exons (i.e. sequences where "exon" occurs consecutively) as valid when comparing with given validator. For example, if the validator is `c("gene", "mRNA", "exon")` and `areMultipleExonsValid = FALSE`, this function will only considerate events as valid if they have the exact same elements. If `areMultipleExonsValid = TRUE`, a valid events could include the elements `c("gene", "mRNA", "exon", "exon", "exon")`.

### Value

Data.frame with valid events

### Examples

    event <- read.table(text = "
     chr1 SE gene 17233 18061  .  -  .
     chr1 SE dkfd 00000 30000  .  -  .
     chr1 SE mRNA 17233 18061  .  -  .
     chr1 SE exon 17233 17368  .  -  .
     chr1 SE exon 17526 17742  .  -  .
     chr1 SE exon 17915 18061  .  -  .
     chr1 SE mRNA 17233 18061  .  -  .
     chr1 SE exon 17233 17368  .  -  .
     chr1 SE exon 17915 18061  .  -  .
     chr1 SE gene 17233 18061  .  -  .
     chr1 SE mRNA 17233 18061  .  -  .
     chr1 SE exon 17233 17368  .  -  .
     chr1 SE exon 17606 17742  .  -  .
     chr1 SE exon 17915 18061  .  -  .
     chr1 SE mRNA 17233 18061  .  -  .
     chr1 SE exon 17233 17368  .  -  .
     chr1 SE exon 17915 18061  .  -  .
    ")
    validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
    psichomics:::getValidEvents(event, validator)

[Package psichomics version 1.6.2 Index]