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 based on the `validator`. For example, if `validator = c("gene", "mRNA", "exon")` and `areMultipleExonsValid = FALSE`, the event `c("gene", "mRNA", "exon", "exon")` is not valid as it has one additional exon. If `areMultipleExonsValid = TRUE`, the same event would be valid.

### 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 1.14.1 Index]