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Jacquard (version 1.0.2)

Estimation of Jacquard's Genetic Identity Coefficients

Description

Contains procedures to estimate the nine condensed Jacquard genetic identity coefficients (Jacquard, 1974) by constrained least squares (Graffelman et al., 2024) and by the method of moments (Csuros, 2014) . These procedures require previous estimation of the allele frequencies. Functions are supplied that estimate relationship parameters that derive from the Jacquard coefficients, such as individual inbreeding coefficients and kinship coefficients.

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Version

Install

install.packages('Jacquard')

Monthly Downloads

169

Version

1.0.2

License

GPL (>= 2)

Maintainer

Jan Graffelman

Last Published

September 17th, 2024

Functions in Jacquard (1.0.2)

CalculateMom

Calculate Moment Estimators for Relatedness Parameters
Jacquard.cls

Estimation of Jacquard coefficients by Constrained Least Squares
JointGenotypeCounts

Calculate joint pairwise Genotype Counts
mafvector

Calculate the Minor Allele Frequency (MAF) for a matrix with (0,1,2) genotype data
SimulatedPedigree

Simulated SNP data according to a Pedigree
CalculateTheta

Calculate Relatedness Paramenters from Jacquard Coefficients tA Capitalized Title (ideally limited to 65 characters)
PairwiseList

Create a Pairwise List of Jacquard Coefficients
MakeM

Create matrix of conditional joint genotype probabilities
DeltaPair

Extract estimates of Jacquard coefficients for a given pair
BoxplotDelta

Boxplots of Jacquard Coefficients
BoxplotTheta

Boxplots of Relateness parameters
GTC

Joint Genotype Counts according to a Pedigree
DeltaSimulatedPedigree

Estimates of Jacquard Coefficients for Simulated SNP data according to a Pedigree