extract_IsoSeq_ge: Extract the sequence around splice sites based on genome.

In BMILAB/AStrap: Identificantion of alternative splicing events and classificaiton of alternative splicing types

Description

A function for extracting a set of subsequences surrounding splice sites from a sequence container like a BSgenome or XStraingSet.

Usage

extract_IsoSeq_ge(ASdata, genome)

Arguments

ASdata	A data frame holds an alternative splicing database, including intron retention (IR), exon skipping (ES), alternative donor sites (AltD), and alternative acceptor sites (AltA).
genome	A BSgenome or XStringSet object.

Value

A alternative splicing data frame with sequence information.

Examples

##Load the rice genome (MSU)
library("BSgenome.Osativa.MSU.MSU7")

##Load the alternative splicing database
path <- system.file("extdata","sample_riceAS.txt",
                     package = "AStrap")
rice_ASdata <-read.table(path,sep="\t",head = TRUE,
                         stringsAsFactors = FALSE)

##Extract the sequence around splice sites based on genome
AS.data <- extract_IsoSeq_ge(rice_ASdata,Osativa)

BMILAB/AStrap documentation built on Nov. 20, 2020, 4:03 p.m.