Multi-Locus Geno-Typing

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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