MIG: MIG algorithm for computation of haplotype blocks

In xthchen/haplotest: Haplotype based testing for evolve and resequence

MIG algorithm for computation of haplotype blocks

Description

Algorithm for computation of haplotype blocks, from (Taliun, D. et al. 2014).

Usage

MIG(
  haplotype,
  frequency_matrix,
  allele_frequency,
  LDU = 0.98,
  LDL = 0.7,
  EHR = 0.9,
  d = 0.95
)

Arguments

haplotype	Binary numeric matrix containing information of haplotype structure. The columns corresponds to the haplotypes and the rows to the SNPs.
frequency_matrix	Numeric matrix, with each i,j element being the frequency of haplotype i at sequenced time point j.
allele_frequency	Numeric matrix, with each i,j element being the frequency of SNP i at sequenced time point j.
LDU	Numeric, parameter compared to upper 90 % confidence interval for normalised LD variance, chosen in line with Gabriel, S. B. et al. (2002)
LDL	Numeric, parameter compared to lower 90 % confidence interval for normalised LD variance, chosen in line with Gabriel, S. B. et al. (2002)
EHR	Numeric, parameter for showing strong evidence of historical recombination, chosen in line with Gabriel, S. B. et al. (2002)
d	Numeric, parameter regarding haplotype block, chosen in line with Gabriel, S. B. et al. (2002)

Value

Numeric matrix of filtered haplotype block candidates, with the first column being the starting SNP position of the candidate, and second column ending SNP position of the candidate. Each row will corresponds to a single candidate.

References

Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E. S., Daly, M. J., Altshuler, D., (2002), The structure of haplotype blocks in the human genome, Science 296(5576): 2225–2229.

Taliun, D., Gamper, J., Pattaro, C., (2014), Efficient haplotype block recognition of very long and dense genetic sequences, BMC bioinformatics 15: 10.

See Also

haplotest()

xthchen/haplotest documentation built on Nov. 29, 2022, 12:07 p.m.