define_haplotypes {HaploVar} | R Documentation |
Define Haplotypes
Description
This function requires a VCF and an LD matrix. It will then define local haplotypes and return a list of tables. Each table within the list represents one haplotype. These haplotype tables display the SNP genotypes within the haplotype.
Usage
define_haplotypes(
vcf,
LD,
epsilon = 0.6,
MGmin = 30,
hetmiss_as = "allele",
keep_outliers = FALSE
)
Arguments
vcf |
A VCF file. |
LD |
A LD matrix file. |
epsilon |
Affects haplotype size. It is a parameter of the DBSCAN clustering tool. The default is 0.6. |
MGmin |
The minimum number of SNPs within a cluster for it to be defined as a haplotype.The default is 30. |
hetmiss_as |
Affects how missing data is handled for all instances where one allele in a genotype is missing.If hetmiss_as = "allele" the genotype is assumed to be heterozygous. If hetmiss_as = "miss" the genotype is treated as NA. |
keep_outliers |
If FALSE, removes SNPs that are determined to be outliers. |
Value
A list of haplotype tables.