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| 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 |