MCN.frequencies.list: Example model adequacy dataset

In gbradburd/SpaceMix: Runs SpaceMix: a method for inferring and visualizing patterns of population genetic structure

Example model adequacy dataset

Description

Example output of processed (mean-centered and normalized) allele frequency data produced by running a SpaceMix analysis

Usage

MCN.frequencies.list

Format

A list with 5 elements

mean.sample.sizes

vector of mean sample sizes for all samples with length = number of samples

sample.frequencies

matrix of sample frequencies (counts/sample.sizes) with nrow = number of samples and ncol = number of loci.

normalized.sample.frequencies

matrix of sample frequencies normalized by mean.f * (1-mean.f), where mean.f at a locus is the mean alelle frequency at that locus

mean.centered.sample.frequencies

matrix of sample frequencies with the mean allele frequency at each locus subtracted from all entries at that locus

mean.centered.normalized.sample.frequencies

matrix of sample frequencies that is both normalized and mean-centered as described above.

gbradburd/SpaceMix documentation built on Oct. 19, 2022, 12:43 p.m.