extractSpliceEvents {SPLINTER} | R Documentation

## extractSpliceEvents

### Description

Extracts the location of target, upstream and downstream splice sites Used for calculations and genome visualizations

### Usage

    extractSpliceEvents(
      data = NULL,
      filetype = "mats",
      splicetype = "SE",
      fdr = 1,
      inclusion = 1,
      start0 = TRUE
    )

### Arguments

`data` | character. path to file
`filetype` | character. type of splicing output. c('mats','custom'). see Details.
`splicetype` | character. c('SE', 'RI', 'MXE', 'A5SS', 'A3SS')
`fdr` | numeric. false discovery rate filter range [0,1]
`inclusion` | numeric. splicing inclusion range, takes absolute value
`start0` | boolean 0-base start

### Details

filetype 'custom' should provide a 9-column tab-delimited text file with the following columns: ID (Ensembl gene id), Symbol (gene name), chr, strand, exonStart, exonEnd, exon2Start, exon2End, upstreamStart, upstreamEnd, downstreamStart, downstreamEnd eg. ENSG0000012345 chr1 + 3 4 5 6 1 2 7 8

### Value

list containing information on
(1) original file type
(2) splice event type
(3) data.frame with splicing regions

### Author(s)

Diana Low

### See Also

http://rnaseq-mats.sourceforge.net/user_guide.htm for MATS file definition

### Examples

    data_path<-system.file("extdata",package="SPLINTER")
    splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))

[Package SPLINTER version 1.16.0 Index]