extractRef: Process the line contening the reference sequence

Description Usage Arguments Value Author(s) Examples

View source: R/prepareHLAdb.R

Description

Extract the information about the reference sequence.

Usage

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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

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## 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.