getValidEvents: Filters the events with valid elements according to the given...

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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)

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.