extractSeq: Process the line containing the alignment to the reference

Description Usage Arguments Value Author(s) Examples

View source: R/prepareHLAdb.R

Description

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

Usage

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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

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## 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.