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mlgt (version 0.16)

Multi-Locus Geno-Typing

Description

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.

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Install

install.packages('mlgt')

Monthly Downloads

4

Version

0.16

License

GPL (>= 2)

Maintainer

Dave T Gerrard

Last Published

March 26th, 2012

Functions in mlgt (0.16)

mlgt: Multi-locus geno-typing

Make genotype calls

createKnownAlleleList

Create variantMap object from allele alignment

getTopBlastHits

Return top blast hits

plotGenotypeEvidence

Plot genotyping evidence

writeGenotypeCallsToFile

Write genotype calls to file

Prepare to run mlgt

callGenotypes.default

Default internal methods for callGenotypes

dumpVariantMap.mlgtResult

Dump variants as fasta

An example mlgtResult object.

An S4 class to hold results from mlgt

combineMlgtResults

Combine two or more mlgtResult objects

printBlastResultGraphs

Plot BLAST statistics for several markers to file

Alignment error correction

Report on alignment

Results from callGenotypes

getSubSeqsTable

Align and trim sequences for marker/sample pair

inspectBlastResults

Plot BLAST statisitics for one marker

Print sequence to file

An S4 class to hold all unique variants found/known for a marker.

Get variants for all markers/samples

An S4 class that holds information about an mlgt analysis.