extractSpliceEvents: extractSpliceEvents

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/main_splinter.R

Description

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

Usage

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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

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

SPLINTER documentation built on Nov. 17, 2017, 11:11 a.m.