extractSpliceSites: extractSpliceSites

In dianalow/SPLINTER: Splice Interpreter of Transcripts

extractSpliceSites

Description

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

Usage

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

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")

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