Package: mixIndependR 1.0.0

Bing Song

mixIndependR: Genetics and Independence Testing of Mixed Genetic Panels

Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.

Authors:Bing Song

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mixIndependR.pdf |mixIndependR.html✨
mixIndependR/json (API)
NEWS

# Install 'mixIndependR' in R:
install.packages('mixIndependR', repos = c('https://ice4prince.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ice4prince/mixindependr/issues

Datasets:
  • mixexample - Genotype Data from A Selected Mix Panel

On CRAN:

22 exports 2 stars 1.10 score 1 dependencies 1 mentions 8 scripts 242 downloads

Last updated 3 years agofrom:21041d4b85. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 25 2024
R-4.5-winOKAug 25 2024
R-4.5-linuxOKAug 25 2024
R-4.4-winOKAug 25 2024
R-4.4-macOKAug 25 2024
R-4.3-winOKAug 25 2024
R-4.3-macOKAug 25 2024

Exports:AlleleFreqAlleleShareComposPare_KComposPare_XcountaDist_SimuChisqDistAlleleShareDistHeteroExpProAlleleShareFreqAlleleShareFreqHeteroGenotypeFreqHeterozygousHWE.ChisqmixIndependKmixIndependXread_vcf_gtRealProAlleleShareRxpHeteroSimulate_DistKSimulate_DistXsplitGenotype

Dependencies:data.table

Basic Genetics

Rendered fromBasicGenetics.Rmdusingknitr::rmarkdownon Aug 25 2024.

Last update: 2020-12-14
Started: 2020-11-22

Distribution Building and Comparison

Rendered fromDistributionBuildingNComparison.Rmdusingknitr::rmarkdownon Aug 25 2024.

Last update: 2020-12-14
Started: 2020-11-22

Hypothesis Test

Rendered fromHypothesisTest.Rmdusingknitr::rmarkdownon Aug 25 2024.

Last update: 2020-12-14
Started: 2020-11-22

Readme and manuals

Help Manual

Help pageTopics
Calculate Allele FrequencyAlleleFreq
Calculate numbers of sharing alleles each pair at each locusAlleleShare
Generate Comparison Observed and Expected No. of Heterozygous Loci.ComposPare_K
Generate Comparison Observed and Expected No. of Shared Alleles.ComposPare_X
Simple count including zero###counta
Build a simulated distribution for Chi-SquareDist_SimuChisq
Build Expected Distribution of Numbers of Shared AllelesDistAlleleShare
Build Expected Distribution of Numbers of Heterozygous LociDistHetero
Calculate the Expected Probability of 0,1 and 2 Shared Alleles###ExpProAlleleShare
Build Observed Distribution of No. of Shared AllelesFreqAlleleShare
Build Observed Distribution of No. of Heterozygous lociFreqHetero
Calculate Genotype Frequency###GenotypeFreq
Test heterozygosity at each locusHeterozygous
Test the Hardy Weinberg Equilibrium with Chi-square test####HWE.Chisq
Genotype Data from A Selected Mix Panelmixexample
Quick pvalue of total number of heterozygous locimixIndependK
Quick pvalue of total number of shared allelesmixIndependX
Import genotype data from vcf files/read_vcf_gt
Calculate the Real Probability of 0,1 and 2 Shared Alleles###RealProAlleleShare
Calculate Real or Expected Average Heterozygosity at each locusRxpHetero
Generate a Bundle of Simulated distributions for No. of heterozygous loci with known heterozygositesSimulate_DistK
Build a simulated distribution for No. of Shared AllelesSimulate_DistX
Split Genotype Table to Duo-Allele TablesplitGenotype