Identify and subset loci with any heterozygous parent genotype.

Identify and subset loci with any heterozygous parent genotype.

Usage

parent_het(x, rp_row, dp_row, sep = ":", na_code = NA)

Arguments

x

A data matrix or frame with markers as columns and samples as rows.

rp_row, dp_row

An integer or character value indicating the row index or name of Parent 1 and 2.

sep

A character used as separator for genotype calls, default is a colon.

na_code

A value indicating missing data in x.

Value

A list object with the following components: 1) data frame of loci with at least one hetrozygous parent genotype, if present. 2) data frame of loci with all homozygous parent genotype.

Examples

# example code
library(panGenomeBreedr)

# Marker data
dat <- data.frame(snp1 = c('C:A', 'A:A', 'C:A', 'C:A'),
                  snp2 = c('C:C', 'G:G', 'C:C', 'C:C'),
                  snp3 = c('C:T', 'C:C', 'C:T', 'C:T'),
                  snp4 = c('G:G', '-:-', 'G:-', 'G:G'),
                  snp5 = c('T:T', 'A:A', 'T:A', 'T:A'),
                  row.names = c('rp', 'dp', 'ind_1', 'ind_2'))

# Find loci with at least one heterozygous parent genotype
par_het <- parent_het(x = dat,
                      rp_row = 1,
                      dp_row = 2,
                      sep = ':')$par_het