createKnownAlleleList: Create 'variantMap' object from allele alignment

In mlgt: Multi-Locus Geno-Typing

Description

Create a variantMap object to store known alleles for a marker

Usage

  createKnownAlleleList(markerName, markerSeq,
    alignedAlleleFile, alignFormat = "msf",
    sourceName = alignedAlleleFile, userAlignment = FALSE)

Arguments

markerName	A specific marker name
markerSeq	something
alignedAlleleFile	a sequence alignment
alignFormat	the format of alignedAlleleFile. "msf" (the default) or "fasta"
sourceName	A character string to record the source of the alignment. Defaults to the value of alignedAlleleFile
userAlignment	The specified 'alignedAlleleFile' already includes the marker sequence. Default = FALSE.

Details

To compare variants produced using mlgt the sequences of the known alleles must be aligned to the same marker used to find the variants. The resulting sub-sequence alignment may have identical sequences for different alleles. If that happens, those alleles are condensed into one and their names concatenated. User can supply files with marker sequences pre-aligned to the reference alleles.

Value

a variantMap object named by markerName

mlgt documentation built on May 1, 2019, 8:45 p.m.