make_Q: Calculate ancestry coefficients

In gnrobinson/cloneR: Identifying clonal groups to aid clone correction in population-based studies

Calculate ancestry coefficients

Description

This function creates individual ancestry coefficients (implemented through LEA) of subsetted .geno files. The subsetted .geno files are located in 'subsets/'.

Usage

make_Q(K, CPU = 1, alpha = 10, tolerance = 1e-05, iterations = 200, ploidy = 2)

Arguments

K	The K value (or range) used to calculate ancestry matrix
CPU	A number of CPUs to run the parallel version of the algorithm (LEA)
alpha	A numeric value corresponding to the snmf regularization parameter (LEA)
tolerance	A numeric value for the tolerance error (LEA)
iterations	An integer for the maximum number of iterations in SNMF algorithm (LEA)
ploidy	1 if haploid, 2 if diploid, n if n-ploid
plot	TRUE/FALSE: Plots relationships between isolates visually

Value

.Q file

Examples

make_Q(K = 2:20, CPU = 1, alpha = 10, tolerance = 1e-05, iterations = 200, ploidy = 2)

gnrobinson/cloneR documentation built on Feb. 8, 2024, 7:46 a.m.