makeROI: makeROI

In SPLINTER: Splice Interpreter of Transcripts

Description

Creates an object to store information about the splice site (region of interest) including flanking regions and alternative splice outcome

Usage

makeROI(df, type = "SE")

Arguments

df	data.frame object from extractSpliceEvents
type	type of splicing event c("SE","RI","MXE","A5SS","A3SS")

Value

a list containing
(1) type : splice type
(2) name : ID of transcript
(3) roi : GRanges object of splice site
(4) flank : GRanges object of flanking exons of splice site
(5) roi_range : GRangesList of splice site and it's alternative outcome based on type

Author(s)

Diana Low

Examples

single_record<-splice_data$data[which(grepl("Prmt5",splice_data$data$Symbol)),]
roi <- makeROI(single_record,type="SE")

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