Importing Genetic Data into Coala

In coala: A Framework for Coalescent Simulation

While coala primiary focuses on simulation of data, it also offers to calculate summary statsitcs from real data. This is particularly useful when comparing the statistics of real and simulated data.

Rather than offering functions to import data directly, coala can convert the internal formats of other R packages into its own format. Currently, the PopGenome package is supported, but we plan to support ape and pegas in the future.

Importing Data from PopGenome

PopGenome provides functions for reading various data formats, including vcf and fasta. Please refer to its documentation for detailed instructions. As an example, we will read sequence data from a short fasta file that is included in coala:

suppressPackageStartupMessages(library(PopGenome))
fasta <- system.file("example_fasta_files", package = "coala")
data_pg <- readData(fasta, progress_bar_switch = FALSE)
data_pg <- set.outgroup(data_pg, c("Individual_Out-1", "Individual_Out-2"))
individuals <- list(paste0("Individual_1-", 1:5), paste0("Individual_2-", 1:5))
data_pg <- set.populations(data_pg, individuals)

Here the sequences originate from two population and an outgroup. The outgroup is required for most summary statistics.

We can now convert data_pg using the as.segsites function:

library(coala)
segsites <- as.segsites(data_pg)

Next, we calculate summary statistics using calc_sumstats_from_data:

model <- coal_model(c(5, 5, 2), 1, 25) + 
  feat_mutation(5) +
  feat_outgroup(3) +
  sumstat_sfs(population = 1)
stats <- calc_sumstats_from_data(model, segsites)
stats$sfs

Alternatively, it is also possible to pass the data_pg object directly to calc_sumstats_from_data:

stats <- calc_sumstats_from_data(model, data_pg)
stats$sfs

Please refer to the help pages for as.segsites and calc_sumstats_from_data for additional information.

coala documentation built on May 29, 2024, 11:14 a.m.