cal_lda {LDAandLDAS}

LDA of a pair of SNPs

Description

Computation of the pairwise Linkage Disequilibrium of Ancestry (LDA) between a pair of single nucleotide polymorphisms (SNPs).

Usage

cal_lda(data_resample, data_base, data_experiment, n_ancestry)

Arguments

data_resample

a data frame of the first SNP's ancestry probabilities after resampling. Different ancestry probabilities are in different columns.

data_base

a data frame of the first SNP's ancestry probabilities. Different ancestry probabilities are in different columns.

data_experiment

a data frame of the second SNP's ancestry probabilities. Different ancestry probabilities are in different columns.

n_ancestry

a positive integer representing the number of different ancestries.

Details

This function computes the LDA between two SNPs. Resampling of one of the SNPs' painting data is required prior to implementing this function. To compute pairwise LDA between multiple pairs of SNPs, please use LDA.

Value

a numeric number representing the pairwise LDA of the two SNPs.

References

Barrie, W., Yang, Y., Irving-Pease, E.K. et al. Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations. Nature 625, 321–328 (2024).

Examples

# compute the LDA between the 50th SNP and the 55th SNP
# painting data for the 50th SNP (2 ancestries)
data_base <- cbind(LDAandLDAS::example_painting_p1[,50],
                   LDAandLDAS::example_painting_p2[,50])

# painting data for the 55th SNP (2 ancestries)
data_experiment <- cbind(LDAandLDAS::example_painting_p1[,55],
                         LDAandLDAS::example_painting_p2[,55])

# resample painting data for the 50th SNP
data_resample <- data_base[sample(1:nrow(data_base)),]

#compute their pairwise LDA
LDA_value <- cal_lda(data_resample,data_base,data_experiment,2)