get.pattern.variants: get.pattern.variants

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

get.pattern.variants

Description

Given a vector of strains names and a set of varaints, return the variants for which the given strains have one allele and the remaining strains have the other allele.

Usage

  get.pattern.variants(variants, strain.subset = NULL)

Arguments

variants	Matrix of data.frame of variants with four header columns containing annotation and snps in the remaining columns.
strain.subset	character vector of strain names that comprise one subset.

Details

Use this function to obtain a subset of SNPs for which one set of strains contain one allele and the rest contain the other allele. This might come up in the course of QTL mapping where several strains have a high allele and others have a low allele.

Value

Data.frame of variants that match the requested pattern.

Author(s)

Daniel Gatti

See Also

get.variants

Examples

  ## Not run: 
    vcf = readVcf("vcf_file.tar.gz", param)
    snp.subset = get.pattern.variants(vcf, 
    strain.subset = c("A/J", "NOD/ShiLtJ", "NZO/HlLtJ", "AKR/J"))
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.