extractSpliceEvents: extractSpliceEvents

In dianalow/SPLINTER: Splice Interpreter of Transcripts

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=""))

dianalow/SPLINTER documentation built on March 28, 2024, 2:07 p.m.