DetectEvents {MARVEL}

Detect Splicing Events

Description

Detects splicing events, specifically alternative first and last exons (AFE, ALE) from GTF. This is a wrapper function for DetectEvents.ALE and DetectEvents.AFE functions.

Usage

DetectEvents(
  MarvelObject,
  min.cells = 50,
  min.expr = 1,
  track.progress = FALSE,
  EventType
)

Arguments

MarvelObject

Marvel object. S3 object generated from CreateMarvelObject function.

min.cells

Numeric value. The minimum number of cells in which the gene is expressed for the gene to included for splicing event detected and quantification. To be used in conjunction with min.expr argument. Default value is 50.

min.expr

Numeric value. The minimum expression value for the gene to be considered to be expressed in a cell. Default value is 1.

track.progress

Logical. If set to TRUE, progress bar will appear to track the progress of the rate-limiting step of this function, which is the extraction of the final exon-exon junctions. Default value is FALSE. Only applicable when EventType set to "ALE" or "AFE".

EventType

Character string. Indicate which splicing event type to calculate the PSI values for. Can take value "ALE" or "AFE".

Value

An object of class S3 with new slot MarvelObject$SpliceFeature$ALE or MarvelObject$SpliceFeature$AFE.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- DetectEvents(MarvelObject=marvel.demo,
                            min.cells=5,
                            min.expr=1,
                            track.progress=FALSE,
                            EventType="AFE"
                            )