Description Usage Arguments Value See Also
vcf_to_matrix
converts variant calls from a bcf, vcf.gz or vcf file into an R dataframe.
Uses only biallelic variants. Heterozygous calls are ignored. Requires bcftools.
1 | vcf_to_matrix(vcf, allele_freq = 0, tag_snps = NA, region = NA)
|
vcf |
a bcf, vcf, or vcf.gz file |
allele_freq |
allele frequency to filter on. Default is 0 |
region |
A region to subset on. |
tag_snips |
A set of variants to filter on. By default, all variants are taken. |
Matrix of genotype calls
generate_kinship generate_mapping
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