GeneIdentityMatrix: Gene Identity Matrix

In pooledpeaks: Genetic Analysis of Pooled Samples

Gene Identity Matrix

Description

Using the number of typed loci, this function calculates the gene identity between all possible pairwise combinations between individuals for all markers creating a matrix.

Usage

GeneIdentityMatrix(RawData = data.frame, LociGenotyped = matrix)

Arguments

RawData	A data frame containing the input data must be in LoadData style LoadData.
LociGenotyped	The Output from the TypedLoci function

Value

The Gene Identity Matrix

Examples

genetic_data <- data.frame(
Locus = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2),
Locus_allele = c("Marker1", "n", 1, 2, 3, "Marker2", "n", 1, 2, 3),
Sample1 = c(NA, 10, 0.5, 0.5, 0, NA, 10, 0.2, 0.3, 0.5),
Sample2 = c(NA, 20, 0.1, 0.2, 0.7, NA, 20, 0.3, 0.4, 0.3),
Sample3 = c(NA, 30, 0.3, 0.4, 0.3, NA, 30, 0.4, 0.2, 0.4)
)

n_alleles <- matrix(c(
3, 3, 3,
3, 3, 3,
3, 3, 3
), nrow = 3, byrow = TRUE,
dimnames = list(paste0("Sample", 1:3), paste0("Sample", 1:3)))

GeneIdentityMatrix(RawData=genetic_data,LociGenotyped=n_alleles)

pooledpeaks documentation built on April 3, 2025, 10:53 p.m.