R: Multi-Locus Geno-Typing

# Multi-Locus Geno-Typing

## Documentation for package ‘mlgt’ version 0.16

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

mlgt-package | mlgt: Multi-locus geno-typing
alignReport | Report on alignment
callGenotypes | Make genotype calls
callGenotypes.default | Default internal methods for 'callGenotypes'
callGenotypes.mlgtResult | Make genotype calls
combineMlgtResults | Combine two or more mlgtResult objects
createKnownAlleleList | Create 'variantMap' object from allele alignment
dumpVariantMap.mlgtResult | Dump variants as fasta
dumpVariants | Print sequence to file
errorCorrect | Alignment error correction
errorCorrect-method | Alignment error correction
genotypeCall | Results from 'callGenotypes'
getSubSeqsTable | Align and trim sequences for marker/sample pair
getTopBlastHits | Return top blast hits
inspectBlastResults | Plot BLAST statisitics for one marker
mlgt | Get variants for all markers/samples
mlgt-method | Get variants for all markers/samples
mlgt.mlgtDesign | Get variants for all markers/samples
mlgtDesign | An S4 class that holds information about an mlgt analysis.
mlgtResult | An S4 class to hold results from 'mlgt'
my.mlgt.Result | An example 'mlgtResult' object.
plotGenotypeEvidence | Plot genotyping evidence
plotGenotypeEvidence-method | Plot genotyping evidence
plotGenotypeEvidence.genotypeCall | Plot genotyping evidence
plotGenotypeEvidence.genotypeCall.file | Plot genotyping evidence
plotGenotypeEvidence.list | Plot genotyping evidence
prepareMlgtRun | Prepare to run mlgt
prepareMlgtRun-method | Prepare to run mlgt
prepareMlgtRun.listDesign,prepareMlgtRun.mlgtDesign | Prepare to run mlgt
printBlastResultGraphs | Plot BLAST statistics for several markers to file
variantMap | An S4 class to hold all unique variants found/known for a marker.
writeGenotypeCallsToFile | Write genotype calls to file
writeGenotypeCallsToFile-method | Write genotype calls to file
writeGenotypeCallsToFile.list,writeGenotypeCallsToFile.genotypeCall | Write genotype calls to file