hsphase (version 2.0.1)

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

Description

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

Details

Package:	hsphase
Type:	Package
Version:	2.0.1
Date:	2014-6-17
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, M. H., Kinghorn, B. P., van der Werf, J. H., & Gondro, C (2013). Effect of genotype and pedigree error on detection of recombination events, sire imputation and haplotype inference using the hsphase algorithm. In Proc. Assoc. Advmt. Anim. Breed. Genet (Vol. 20, pp. 546-549). AAABG; Napier, New Zealand.

Ferdosi, M. H., Kinghorn, B. P., van der Werf, J. H., & Gondro, C. (2014). Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. Genetics, selection, evolution: GSE, 46(1), 11.

Ferdosi, M. H., Kinghorn, B. P., van der Werf, J. H., Lee, S. H., & Gondro, C. (2014). hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. BMC Bioinformatics, 15(1), 172.

Ferdosi, M. H., & Boerner, V. (2014). A fast method for evaluating opposing homozygosity in large SNP data sets. Livestock Science.

Examples

# NOT RUN {
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))
# }