findCompatibleEvents: findCompatibleEvents

In SPLINTER: Splice Interpreter of Transcripts

Description

Which transcript contains the event? Each event has 2 possibilities, as long as the transcript fulfills one, it passes the test Has to be exact (inner junctions)

Usage

findCompatibleEvents(tx, tx2 = NULL, roi, sequential = TRUE, verbose = FALSE)

Arguments

tx	GRangesList object of transcripts
tx2	optional GRangesList object of transcripts if tx is list of cds
roi	makeROI object contaning event information
sequential	logical. Exons have to appear sequentially to be considered compatible
verbose	logical. printouts and messages.

Details

Seperates into event/region1 and 2 for the alternative case

Value

list of length 4
(1) GRangesList
(2) Hits status [c]=coding; [nc]=non-coding
(3) ct - compatible transcripts
(4) tt - total transcripts

Author(s)

Diana Low

Examples

compatible_cds <- findCompatibleEvents(valid_cds,roi=roi,verbose=TRUE)

SPLINTER documentation built on Nov. 8, 2020, 8:13 p.m.