In chollenbeck/pantomime: Tools for tidy population genetics

knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(adegenet)

{pantomime}

Utilities for tidy population genetics analysis in R

Installation

remotes::install_github("chollenbeck/pantomime")

Data exploration

library(pantomime)
library(related)

data(nancycats) # From adegenet

# Extract allele frequencies from a genind object
cats1 <- nancycats[pop = 1]
df <- get_allele_freqs(cats1)

head(df)

Get locus-by-locus statistics:

cat_stats <- get_locus_stats(cats1, hwe_test = TRUE)

cat_stats

Get locus diversity statistics:

cat_div <- get_locus_diversity(cats1)

cat_div

Quick PCA

Run a quick PCA of the data

pca_tbl <- qpca(cats1)

ggplot(pca_tbl, aes(x = Axis1, y = Axis2, col = pop)) +
  geom_point()

Relatedness

# Calculate relatedness from a genind object
rel <- genind2related(cats1)
coanc <- coancestry(genotype.data = rel$gdata, ritland = 1) # From the 'related' package

# Convert to tibble
rel_tbl <- coanc$relatedness %>%
  as_tibble()

head(rel_tbl)

Quickly visualize the distribution of Ritland relatedness coefficients:

ggplot(rel_tbl, aes(x = ritland)) +
  geom_histogram()

chollenbeck/pantomime documentation built on June 16, 2024, 1:45 a.m.