hsphase (version 1.2.4)

hsphase-package: Phasing, Sire Imputation and Recombination Events for Half-sib Families

Description

Identification of recombination events, haplotype reconstruction and sire imputation using half-sib family SNP data.

Details

ll{ Package: hsphase Type: Package Version: 1.2.4 Date: 2013-5-25 License: GPL 3 }

Main Functions: bmh: Block partitioning ssp: Sire inference aio: Phasing imageplot: Image plot of the block structure rpoh: Reconstruct pedigree based on opposing homozygote

Auxiliary Functions hss: Half-sib family splitter cs: Chromosome splitter para: Parallel Data Analysis Note: These functions can be used to analyse large datasets.

References

Ferdosi MH, Kinghorn BP, JHJ van der Werf, Gondro C: Effect of genotype and pedigree error on block partitioning, sire imputation and haplotype inference using the hsphase algorithm. In: AAABG; Napier, New Zealand. 2013. Ferdosi, MH, BP Kinghorn, JHJ van der Werf and C Gondro (2013). Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. under review Ferdosi, MH, BP Kinghorn, JHJ van der Werf and C Gondro (2013). HSPhase: an R package for detection of recombination events, phasing and imputation of half-sib family groups. under review

Examples

genotype <- matrix(c(
  0,0,0,0,1,2,2,2,0,0,2,0,0,0,
  2,2,2,2,1,0,0,0,2,2,2,2,2,2,
  2,2,2,2,1,2,2,2,0,0,2,2,2,2,
  2,2,2,2,0,0,0,0,2,2,2,2,2,2,
  0,0,0,0,0,2,2,2,2,2,2,0,0,0), ncol=14, byrow=TRUE) 
ssp(bmh(genotype), genotype)
aio(genotype)
imageplot(bmh(genotype), title="ImagePlot example")
rplot(genotype, c(1:14))