mlPhaser: Multi-Locus Haplotype Phasing

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Phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.

Author
Dave T. Gerrard
Date of publication
2012-09-04 13:38:46
Maintainer
Dave T. Gerrard <david.gerrard@manchester.ac.uk>
License
GPL (>= 2)
Version
0.01
URLs

View on CRAN

Man pages

getHaploGroupProb
Get haplotype group probability
getValidHaploGroups
Get haplo groups for a genotype
listGenoToTable
Genotype list to genotype table
listHaploToTable
Haplotype list to Haplotype table.
listValidHaplotypes
List valid haplotypes
mlPhaser-package
mlPhaser
phaseReport
Best/all hapltype groups for a genotype
printHaploGroups
Print haplotype groups
printHaploProbs
Print haplo group probabilities
recurseHaplos
Recurse to get haplo groups
reduceRedundantList
Remove redundant haplotype groups
remGeno
Extract haplotype from genotype
simGenoFromHaplo
Simulate genotypes
tableGenoToList
Convert genotype table to list of lists
tableHaploToList
Haplotype table to haplotype list
testHaploInGeno
Test genotype for presence of haplotype

Files in this package

mlPhaser
mlPhaser/MD5
mlPhaser/vignettes
mlPhaser/vignettes/mlPhaser.Rnw
mlPhaser/R
mlPhaser/R/mlPhaser.R
mlPhaser/NAMESPACE
mlPhaser/man
mlPhaser/man/testHaploInGeno.Rd
mlPhaser/man/tableHaploToList.Rd
mlPhaser/man/tableGenoToList.Rd
mlPhaser/man/simGenoFromHaplo.Rd
mlPhaser/man/remGeno.Rd
mlPhaser/man/reduceRedundantList.Rd
mlPhaser/man/recurseHaplos.Rd
mlPhaser/man/printHaploProbs.Rd
mlPhaser/man/printHaploGroups.Rd
mlPhaser/man/phaseReport.Rd
mlPhaser/man/mlPhaser-package.Rd
mlPhaser/man/listValidHaplotypes.Rd
mlPhaser/man/listHaploToTable.Rd
mlPhaser/man/listGenoToTable.Rd
mlPhaser/man/getValidHaploGroups.Rd
mlPhaser/man/getHaploGroupProb.Rd
mlPhaser/inst
mlPhaser/inst/doc
mlPhaser/inst/doc/mlPhaser.Rnw
mlPhaser/inst/doc/mlPhaser.pdf
mlPhaser/DESCRIPTION