R: Create 'variantMap' object from allele alignment

createKnownAlleleList {mlgt} | R Documentation

## Create `variantMap` object from allele alignment

### 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

[Package mlgt version 0.16 Index]