load_popgenWindows: Load a results file from Simon Martin's popgenWindows.py...

In nwvankuren/gwplotting: Utilities for plotting statistics from genome-wide analyses

Description

This function was developed strictly following his GitHub description of the output file. The columns in this output file will vary depending on how many populations you specify. It is up to you to determine what are the necessary columns to keep. Minimally, the output from that script is: scaffold, start, end, mid, sites, pi_popA, pi_popB, dxy_popA_popB, Fst_popA_popB. But you may have all the pairwise comparisons for each specified populations. This function will return all of the statistic columns.

Usage

load_popgenWindows(file, position = "midpoint", min_sites = 0)

Arguments

file	Input file name
position	Use the start, end, or midpoint as the position?
min_sites	Minimum number of sites required for window inclusion.

Value

A tibble.

Examples

a <- system.file("extdata", "test.popgen.csv.gz",
                 package = "gwplotting")
b <- load_popgenWindows( a )
b

nwvankuren/gwplotting documentation built on April 17, 2021, 2:37 p.m.