mlgt: Multi-Locus Geno-Typing

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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.

Author
Dave T. Gerrard
Date of publication
2012-03-26 13:20:25
Maintainer
Dave T. Gerrard <david.gerrard@manchester.ac.uk>
License
GPL (>= 2)
Version
0.16
URLs

View on CRAN

Man pages

alignReport
Report on alignment
callGenotypes
Make genotype calls
callGenotypes.default
Default internal methods for 'callGenotypes'
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-methods
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
mlgtDesign
An S4 class that holds information about an mlgt analysis.
mlgt-methods
Get variants for all markers/samples
mlgt-package
mlgt: Multi-locus geno-typing
mlgtResult
An S4 class to hold results from 'mlgt'
my.mlgt.Result
An example 'mlgtResult' object.
plotGenotypeEvidence-methods
Plot genotyping evidence
prepareMlgtRun-methods
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...
writeGenotypeCallsToFile-methods
Write genotype calls to file

Files in this package

mlgt
mlgt/MD5
mlgt/R
mlgt/R/mlgt.R
mlgt/NAMESPACE
mlgt/man
mlgt/man/writeGenotypeCallsToFile-methods.Rd
mlgt/man/variantMap.Rd
mlgt/man/printBlastResultGraphs.Rd
mlgt/man/prepareMlgtRun-methods.Rd
mlgt/man/plotGenotypeEvidence-methods.Rd
mlgt/man/my.mlgt.Result.Rd
mlgt/man/mlgtResult.Rd
mlgt/man/mlgtDesign.Rd
mlgt/man/mlgt-package.Rd
mlgt/man/mlgt-methods.Rd
mlgt/man/inspectBlastResults.Rd
mlgt/man/getTopBlastHits.Rd
mlgt/man/getSubSeqsTable.Rd
mlgt/man/genotypeCall.Rd
mlgt/man/errorCorrect-methods.Rd
mlgt/man/dumpVariants.Rd
mlgt/man/dumpVariantMap.mlgtResult.Rd
mlgt/man/createKnownAlleleList.Rd
mlgt/man/combineMlgtResults.Rd
mlgt/man/callGenotypes.Rd
mlgt/man/callGenotypes.default.Rd
mlgt/man/alignReport.Rd
mlgt/inst
mlgt/inst/tableOfSampleBarcodeMapping.tab
mlgt/inst/sampleSequences.fasta
mlgt/inst/namedBarcodesFull.fasta
mlgt/inst/namedBarcodes.fasta
mlgt/inst/marker.imgt.msf.list.tab
mlgt/inst/HLA_namedMarkers.fasta
mlgt/inst/HLA_intersectMarkersDec11.fasta
mlgt/inst/doc
mlgt/inst/doc/mlgt_README_0_16.R
mlgt/inst/doc/mlgt_README_0_16.pdf
mlgt/DESCRIPTION
mlgt/data
mlgt/data/mlgtResult.rda
mlgt/CHANGELOG.txt