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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

The dataset imported can be genotype data with sample ID in each row and the marker name in each column.Excel, csv, and vcf files are compatible.

library(mixIndependR)

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Version

Install

install.packages('mixIndependR')

Monthly Downloads

200

Version

1.0.0

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

2

Forks

0

Maintainer

Bing Song

Last Published

March 17th, 2021

Functions in mixIndependR (1.0.0)

mixIndependK

Quick pvalue of total number of heterozygous loci
RxpHetero

Calculate Real or Expected Average Heterozygosity at each locus
Simulate_DistK

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

Genotype Data from A Selected Mix Panel
Simulate_DistX

Build a simulated distribution for No. of Shared Alleles
counta

Simple count including zero###
read_vcf_gt

Import genotype data from vcf files/
mixIndependX

Quick pvalue of total number of shared alleles
RealProAlleleShare

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

Test heterozygosity at each locus
HWE.Chisq

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

Calculate Genotype Frequency###
DistHetero

Build Expected Distribution of Numbers of Heterozygous Loci
splitGenotype

Split Genotype Table to Duo-Allele Table
ComposPare_K

Generate Comparison Observed and Expected No. of Heterozygous Loci.
AlleleFreq

Calculate Allele Frequency
FreqAlleleShare

Build Observed Distribution of No. of Shared Alleles
Dist_SimuChisq

Build a simulated distribution for Chi-Square
ComposPare_X

Generate Comparison Observed and Expected No. of Shared Alleles.
AlleleShare

Calculate numbers of sharing alleles each pair at each locus
ExpProAlleleShare

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

Build Expected Distribution of Numbers of Shared Alleles
FreqHetero

Build Observed Distribution of No. of Heterozygous loci