mlgt: Multi-Locus Geno-Typing

Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

AuthorDave T. Gerrard
Date of publication2012-03-26 13:20:25
MaintainerDave T. Gerrard <david.gerrard@manchester.ac.uk>
LicenseGPL (>= 2)
Version0.16
http://personalpages.manchester.ac.uk/staff/David.Gerrard/

View on CRAN

Functions

alignReport Man page
callGenotypes Man page
callGenotypes.default Man page
callGenotypes.mlgtResult Man page
combineMlgtResults Man page
createKnownAlleleList Man page
dumpVariantMap.mlgtResult Man page
dumpVariants Man page
errorCorrect Man page
errorCorrect,missing,list-method Man page
errorCorrect,mlgtResult,missing-method Man page
genotypeCall Man page
getSubSeqsTable Man page
getTopBlastHits Man page
inspectBlastResults Man page
mlgt Man page
mlgtDesign Man page
mlgt.mlgtDesign Man page
mlgt,mlgtDesign-method Man page
mlgt-package Man page
mlgtResult Man page
my.mlgt.Result Man page
plotGenotypeEvidence Man page
plotGenotypeEvidence.genotypeCall Man page
plotGenotypeEvidence.genotypeCall.file Man page
plotGenotypeEvidence,genotypeCall,missing,character-method Man page
plotGenotypeEvidence,genotypeCall,missing,missing-method Man page
plotGenotypeEvidence,genoytpeCall,missing,character-method Man page
plotGenotypeEvidence,genoytpeCall,missing,missing-method Man page
plotGenotypeEvidence.list Man page
plotGenotypeEvidence,missing,list,character-method Man page
prepareMlgtRun Man page
prepareMlgtRun.listDesign,prepareMlgtRun.mlgtDesign Man page
prepareMlgtRun,missing,character,character,character,list,list,l Man page
prepareMlgtRun,mlgtDesign,missing,missing,missing,missing,missin Man page
printBlastResultGraphs Man page
variantMap Man page
writeGenotypeCallsToFile Man page
writeGenotypeCallsToFile,list,missing-method Man page
writeGenotypeCallsToFile.list,writeGenotypeCallsToFile.genotypeC Man page
writeGenotypeCallsToFile,missing,genotypeCall-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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