extractSpliceSites: extractSpliceSites

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

View source: R/main_splinter.R

Description

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

Usage

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extractSpliceSites(df, target = "SE", site = "donor", motif_range = c(-3,
  6), start0 = TRUE)

Arguments

df

extractSpliceEvents object

target

the target site to extract. See Details.

site

character donor or acceptor

motif_range

numeric vector of splice position to extract

start0

boolean 0-base start

Details

target : the site to extract the sequence from. It can be either the event in question (SE, RI, MXE - first exon, MXE2 - second exon, A5SSlong, A5SSshort, A3SSlong, A3SSshort, upstream or downstream). If this function is used in conjunction with shapiroDonor or shapiroAcceptor to compute scores, then most likely it will be run twice - once for the event, and the other either up- or downstream as a comparison.

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,target="SE")

SPLINTER documentation built on May 20, 2017, 10:31 p.m.

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