sStateCount {diemr}

R Documentation

Count states in a vector

Description

Counts genomic states in one sample.

Usage

sStateCount(s)

Arguments

s	character vector with elements "_", "0", "1", "2" representing missing data, homozygots for allele 1, heterozygots, and homozygots for allele 2. The vector should represent a single individual.

Details

Summarizes the number of markers that are fixed for an allele in the genome of one individual. This is used to construct the I4 matrix in diem.

Value

Numeric vector of length 4 with counts of "_", "0", "1", "2" respectively.

See Also

emPolarise for changing marker polarity.

Examples

genotype <- c("0", "0", "_", "2", "1", "0", "1")
sStateCount(genotype)
# [1] 1 3 2 1

# calculate state counts for a polarised genotype
sStateCount(emPolarise(genotype, TRUE))
# [1] 1 1 2 3

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