Import population genomics summary statistics

Import windowed population genomics statistics such as FST, pi, Dxy, Watterson's theta, and Tajima's D for tidy ggpop plotting.

Usage

import_stats(dir = NULL, ..., type = c("pixy", "vcftools", "auto"))

Arguments

dir

Directory containing pixy or vcftools result files. Files are auto-discovered by suffix.

...

Optional named files such as pi = "pixy_pi.txt" or fst = "pixy_fst.txt". Relative paths are resolved inside dir.

type

Input format. Supports "pixy", "vcftools", and "auto".

Value

A ggpop_stats data frame with normalized columns: stat, chr, start, end, pos, and value.

Examples

pixy_dir <- system.file("extdata", "Population_genomics_statistics", "pixy", package = "ggpop")
stats <- import_stats(pixy_dir, type = "pixy")
#> Error: `dir` must point to an existing directory.
stats |> plot_stats(stat = c("fst", "pi"), chr = "chr2L")
#> Error: object 'stats' not found