generate_mapping: Generate Mapping variant set

In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

Description

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.

Usage

generate_mapping(vcf, allele_freq = 0,
  tag_snps = paste0(path.package("cegwas"), "/41188.WS245.txt.gz"))

Arguments

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

Value

Mapping Snpset

See Also

vcf_to_matrix generate_mapping

AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.