hsphase-package: Phasing, Pedigree Reconstruction, Sire Imputation and...

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

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.

Author(s)

Mohammad H. Ferdosi <[e-mail]>, Cedric Gondro <[e-mail]> Maintainer: Mohammad H. Ferdosi <[e-mail]>

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

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))

Example output

Loading required package: snowfall
Loading required package: snow
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,]    0    0    0    0    0    1    1    1    0     0     1     0     0     0
[2,]    1    1    1    1    0    0    0    0    1     1     1     1     1     1
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
 [1,]    0    0    0    0    0    1    1    1    0     0     1     0     0
 [2,]    0    0    0    0    1    1    1    1    0     0     1     0     0
 [3,]    1    1    1    1    0    0    0    0    1     1     1     1     1
 [4,]    1    1    1    1    1    0    0    0    1     1     1     1     1
 [5,]    1    1    1    1    9    1    1    1    0     0     1     1     1
 [6,]    1    1    1    1    9    1    1    1    0     0     1     1     1
 [7,]    1    1    1    1    0    0    0    0    1     1     1     1     1
 [8,]    1    1    1    1    0    0    0    0    1     1     1     1     1
 [9,]    0    0    0    0    0    1    1    1    1     1     1     0     0
[10,]    0    0    0    0    0    1    1    1    1     1     1     0     0
      [,14]
 [1,]     0
 [2,]     0
 [3,]     1
 [4,]     1
 [5,]     1
 [6,]     1
 [7,]     1
 [8,]     1
 [9,]     0
[10,]     0

hsphase documentation built on May 2, 2019, 3:44 p.m.