extractRef: Process the line contening the reference sequence

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 reference sequence.

Usage

extractRef(seq, startPos)

Arguments

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

Value

A list with two entries. The first is refSeq which is containing the sequence of the reference. The second is seqDiff is a string representing the alignment format for the current sequence.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## String with the sequence information
sequence <- " DOB*01:01:01:01       MGSGWV PWVVALLVNL TRLDSSMTQG TDSPEDFVIQ"

## Extract sequence information
HLAClustRView:::extractRef(seq=sequence, startPos=20)

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