GenotypeFreq: Calculate Genotype Frequency###

In mixIndependR: Genetics and Independence Testing of Mixed Genetic Panels

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.

Details

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

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.

References

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

Examples

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)

mixIndependR documentation built on March 17, 2021, 5:09 p.m.