getBPstats: Generate genotyped base-pair statistics

In gbradburd/popgenstuff: Handy Functions for PopGen Analysis in R

Description

Generate genotyped base-pair statistics

Usage

getBPstats(stacksFAfile, outPath)

Arguments

stacksFAfile	The filename (with necessary path) of the .fa file output by a STACKS run.
outPath	The filename (with necessary path) of the output object you want to generate.

Value

This function does not return a value. Instead, a named list is saved as a .Robj file at the location designated by the outPath argument. The elements of the list are:

• lociDistn vector of length N, where N is total number of individuals in the dataset, for with the ith element gives the number of base pairs genotyped in exactly i individuals. E.g., the 3rd element of lociDistn gives the number of base pairs genotyped in exactly 3 individuals.

• coGeno a symmetric matrix (dimensions N x N) for which the i,jth element gives the number of base pairs genotyped in both samples i and j.

gbradburd/popgenstuff documentation built on Oct. 16, 2021, 12:05 a.m.