extractSpliceSites

Description

Extracts and formats to bed the location of target, upstream and downstream splice sites

Usage

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extractSpliceSites(file, splicetype = "SE", site = "donor", fdr = 1,
  motif_range = c(-3, 6), inclusion = 0)

Arguments

file

character MATS http://rnaseq-mats.sourceforge.net/ output filename or data.frame output from extractSpliceEvents

splicetype

character either SE (skipped exon) or RI (retained intron)

site

character donor or acceptor

fdr

numeric false discovery rate filter range [0,1]

motif_range

numeric vector of splice position to extract

inclusion

numeric fraction,takes absolute value

Value

GRanges object

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=""))
splice_sites<-extractSpliceSites(splice_data$data)

## or
#splice_sites<-extractSpliceSites(file=paste(data_path,"/skipped_exons.txt",sep=""))