extractSeq: Process the line containing the alignment to the reference

In NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq: HLA typing clustering and visualization based on specific similarity metrics

Description

Extract the information about the alignment compared to the reference sequence.

Usage

extractSeq(seq, startPos)

Arguments

seq	A character string containing the alignment sequence.
startPos	A integer corresponding to the position in the character string where the sequence is starting.

Value

A character string representing the aligment sequence compared to the reference sequence.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Define a alignment sequence string
sequence <- " DOB*01:01:01:02       ------ ---------- ---------- "

## Extract the alignment section
HLAClustRView:::extractSeq(seq=sequence, startPos=20)

NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq documentation built on Nov. 23, 2019, 1:57 a.m.