DetectEvents {MARVEL} | R Documentation |
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 |
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 |
Numeric value. The minimum expression value for the gene to be considered to be expressed in a cell. Default value is |
track.progress |
Logical. If set to |
EventType |
Character string. Indicate which splicing event type to calculate the PSI values for. Can take value |
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"
)