mixIndependR (version 1.0.0)

GenotypeFreq: Calculate Genotype Frequency###

Description

Calculate Genotype Frequency###

Usage

GenotypeFreq(x,sep,expect=TRUE)

Arguments

x

a dataframe of genotype data with rownames of sample ID and column names of markers.

sep

allele separator in the imported genotype data. Note: when using the special character like "|", remember to protect it as "\|"(default).

expect

a logic variable. If expect is true, the function will calculate the expected genotype probabilities. If false, calculate the observed genotype frequencies.

Value

a dataframe of genotype frequencies. Each row denotes each genotype; each column denotes each loci. The order of markers follows x; the genotypes are ordered from homozygous to heterozygous.

Details

This function calculates the observed or expected genotype frequency from dataset and allele frequency.#####

References

Chakraborty, R., Srinivasan, M. R., & Daiger, S. P. (1993, ISSN:0002-9297).

Examples

# NOT RUN {
require(mixIndependR)
x <- data.frame(SNP1=c("A|A","T|T","A|T","A|T"),
                STR1=c("12|12","13|14","13|13","14|15"))
GenotypeFreq(x,"\\|",expect=TRUE)
# }