LEI is a measure of marker informativeness comparing multiple ancestral populations. LEI algorithm can be used for finding ancestry informative markers (AIMs) for two-way and multi-way admixed populations using the reference allele frequency data. The R codes provided here are free to download, use, and distribution for non-commercial purpose.
To compute LEI from the reference genotype-level data, use the R-function
lie_geno(x, y)
where, x = vector of genotypes coded as 0, 1, or 2 based on # of reference alleles, length of x = total numbers of ancestral samples genotyped in the reference panels and y = vector of population membership. Length of y = length of x.
To compute LEI from the reference allele frequency data, use the R-function
lie_freq(k, frq_pop, count_pop)
where, k = number of poulations, frq_pop = a vector of reference allele frequencies for the k populations, count_pop = corresponding population size, a vector of length k.
Yadu Gautam, PhD
Research Associate, Asthma Division
Cincinnati Childrens's Medical Hospital, Cincinnati
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. See LICENSE for more details.
Contact Yadu Gautam at yadu.gautam@cchmc.org or Tesfaye Mersha at tesfaye.mersha@cchmc.org for questions, comments, or suggestions.