R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Data Type

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Functions
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Classification

Results 1 - 10 of 21 found.
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writeGenotypeCallsToFile (Package: mlgt) : Write genotype calls to file

A genotype call table or a list of tables can be written to tab-delimited file(s).

● Data Source: CranContrib
● Keywords:
● Alias: writeGenotypeCallsToFile, writeGenotypeCallsToFile,list,missing-method, writeGenotypeCallsToFile,missing,genotypeCall-method, writeGenotypeCallsToFile.list,writeGenotypeCallsToFile.genotypeCall
● 0 images

variantMap (Package: mlgt) : An S4 class to hold all unique variants found/known for a marker.

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

● Data Source: CranContrib
● Keywords:
● Alias: variantMap
● 0 images

printBlastResultGraphs (Package: mlgt) : Plot BLAST statistics for several markers to file

Plot the BLAST statistics easily for all markers of an mlgtResult object.

● Data Source: CranContrib
● Keywords:
● Alias: printBlastResultGraphs
● 0 images

prepareMlgtRun (Package: mlgt) : Prepare to run mlgt

Required before mlgt is used. Create BLAST databases and assign sequences using BLAST.

● Data Source: CranContrib
● Keywords:
● Alias: prepareMlgtRun, prepareMlgtRun,missing,character,character,character,list,list,list,character,character-method, prepareMlgtRun,mlgtDesign,missing,missing,missing,missing,missing,missing,missing,character-method, prepareMlgtRun.listDesign,prepareMlgtRun.mlgtDesign
● 0 images

plotGenotypeEvidence (Package: mlgt) : Plot genotyping evidence

Plot the distributions of values used in calling genotypes.

● Data Source: CranContrib
● Keywords:
● Alias: plotGenotypeEvidence, plotGenotypeEvidence,genotypeCall,missing,character-method, plotGenotypeEvidence,genotypeCall,missing,missing-method, plotGenotypeEvidence,genoytpeCall,missing,character-method, plotGenotypeEvidence,genoytpeCall,missing,missing-method, plotGenotypeEvidence,missing,list,character-method, plotGenotypeEvidence.genotypeCall, plotGenotypeEvidence.genotypeCall.file, plotGenotypeEvidence.list
● 0 images

mlgtResult (Package: mlgt) : An S4 class to hold results from code{link{mlgt

Extends mlgtDesign

● Data Source: CranContrib
● Keywords:
● Alias: mlgtResult
● 0 images

mlgtDesign (Package: mlgt) : An S4 class that holds information about an mlgt analysis.

Returned by prepareMlgtRun. Used as sole input for mlgt

● Data Source: CranContrib
● Keywords:
● Alias: mlgtDesign
● 0 images

mlgt-package (Package: mlgt) : mlgt: Multi-locus geno-typing

Package:	mlgt
Type:	Package
Version:	0.16
Date:	2012-03-27
Author:	Dave T. Gerrard <david.gerrard@manchester.ac.uk>
License:	GPL (>= 2)
LazyLoad:	yes

Details

mlgt sorts a batch of sequence by barcode and identity to templates. It makes use of external applications BLAST and MUSCLE. Genotypes are called and alleles can be compared to a reference list of sequences. More information about each function can be found in its help documentation.

● Data Source: CranContrib
● Keywords:
● Alias: mlgt-package
● 0 images

mlgt (Package: mlgt) : Get variants for all markers/samples

mlgt Works through all pairs of markers and samples. Aligns variants and trims aligned variants to the marker sequence. Potential 'alleles' are assigned from the most common variants within each sample.

● Data Source: CranContrib
● Keywords:
● Alias: mlgt, mlgt,mlgtDesign-method, mlgt.mlgtDesign
● 0 images

inspectBlastResults (Package: mlgt) : Plot BLAST statisitics for one marker

prepareMlgtRun produces several BLAST tables. It is instructive to plot the BLAST results and assess the performance of different markers.

● Data Source: CranContrib
● Keywords:
● Alias: inspectBlastResults
● 0 images