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mixIndependR

The goal of mixIndependR is to test the mutual independence of mixed genetic markers.

Installation

You can install the released version of mixIndependR from CRAN with:

install.packages("mixIndependR")

Example

Usually the dataset imported are allele frequency data with sample ID in each row and the marker name in each column. Every two columns denote the same marker for diploid like autosomes of human beings.

library(mixIndependR)

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Version

Install

install.packages('mixIndependR')

Monthly Downloads

Version

0.3.0

License

GPL (>= 2)

Maintainer

Bing Song

Last Published

October 7th, 2020

Functions in mixIndependR (0.3.0)

AlleleFreq

Calculate Allele Frequency

DistAlleleShare

Build Expected Distribution of Numbers of Shared Alleles

ComposPare_X

Generate Comparison Observed and Expected No. of Shared Alleles.

Dist_SimuChisq

Build a simulated distribution for Chi-Square

ComposPare_K

Generate Comparison Observed and Expected No. of Heterozygous Loci.

DistHetero

Build Expected Distribution of Numbers of Heterozygous Loci

AlleleShare_Table

Calculate numbers of sharing alleles each pair at each locus

FreqAlleleShare

Build Observed Distribution of No. of Shared Alleles

ExpProAlleleShare

Calculate the Expected Probability of 0,1 and 2 Shared Alleles###

FreqHetero

Build Observed Distribution of No. of Heterozygous loci

HWE.Fisher

Test the Hardy Weinberg Equilibrium with Fisher's exact test###

GenotypeFreq

Calculate Genotype Frequency###

HWE.Chisq

Test the Hardy Weinberg Equilibrium with Chi-square test####

Simulate_DistK

Generate a Bundle of Simulated distributions for No. of heterozygous loci with known heterozygosites

Simulate_DistX

Build a simulated distribution for No. of Shared Alleles

mixIndependX

Quick pvalue of total number of shared alleles

Heterozygous

Test heterozygosity at each locus

counta

Simple count including zero###

mixIndependK

Quick pvalue of total number of heterozygous loci

RxpHetero

Calculate Real or Expected Average Heterozygosity at each locus

RealProAlleleShare

Calculate the Real Probability of 0,1 and 2 Shared Alleles###