extract_IsoSeq_tr: Extract the sequence around splice sites based on transcript.

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 XStraingSet.

Usage

extract_IsoSeq_tr(ASdata, transcriptSeq)

Arguments

ASdata	A data frame holds the coordinate of splice sites with as least three columns: Sname, Sstart, Send. Sname is the name of subject in the pariwise sequence alignment; Sstart is the start of subject in the pairwise sequence alignment; Send is the end of subject in the pairwise sequence;
transcriptSeq	An XStringSet object holds the transcript sequence.

Value

A alternative splicing data frame with sequence information.

Examples

##Loading pairwise alignment data
load(system.file("data","sample_Aligndata.Rdata",package = "AStrap"))
head(Aligndata)

##Loading transcript sequence
trSequence.path <- system.file("extdata","example_TRsequence.fasta",
                              package = "AStrap")
trSequence <-  readDNAStringSet(trSequence.path,format = "fasta")

##Extract sequence around splice site based on the transcript sequence
Aligndata <- extract_IsoSeq_tr(Aligndata,trSequence )
colnames(Aligndata)
head(Aligndata$Ddown10)

head(Aligndata$Aup10)

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