Description Usage Arguments Value See Also
generate_mapping
generates a dataframe suitable for mapping. This function uses bcftools to filter out variants with low allele frequencies <5
the af parameter. Additionally, this function uses a subset of variants from the C. elegans genome that tag haplotype blocks.
Tag SNPs were generated in Andersen 2012 et al. Tag snps used can
be adjusted using a text file that specifies CHROM POS. A custom set of variants can be used with the variants
parameter.
1 2 | generate_mapping(vcf, allele_freq = 0,
tag_snps = paste0(path.package("cegwas"), "/41188.WS245.txt.gz"))
|
vcf |
a bcf, vcf.gz, or vcf file |
allele_freq |
minimum allele frequency. Default is >= 5% |
tag_snps |
A set of variants to filter on. By default, a set of tag snps is used |
Mapping Snpset
vcf_to_matrix generate_mapping
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