convert.variants.to.numeric: convert.variants.to.numeric

In DOQTL: Genotyping and QTL Mapping in DO Mice

Description

Given a matrix or data frame with character ACGT SNP values, convert them to numeric values with the major allele coded as 0 and the minor allele as 1.

Usage

convert.variants.to.numeric(variants)

Arguments

variants

Data frame with four header columns. The SNPs must be in ACGT format in columns 5 through ncol(snps).

Details

This function is used before calling plot.alleles() to convert the SNPs into a numeric form suitable for plotting.

Value

Data.frame of the same dimentions as the snps argument, but with the alleles converted to 0 or 1.

Author(s)

Daniel Gatti

Examples

  data(example.snps)
  numeric.snps = convert.variants.to.numeric(example.snps[1:100,])

DOQTL documentation built on May 6, 2019, 3:09 a.m.