doAllTheThings: Calculate a bunch of popgen stats from a VCF file

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

Description

Calculate a bunch of popgen stats from a VCF file

Usage

doAllTheThings(
  vcfFile,
  lociDistn = NULL,
  coGeno = NULL,
  readDepth = FALSE,
  nPCs = 4,
  outPath
)

Arguments

vcfFile	The filename (with necessary path) of the VCF file you want to read into R.
lociDistn	A vector of length N, where N is the number of genotyped individuals, for which 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. Default is NULL.
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. The order of samples in this matrix must be the same as the order of samples in the VCF file. If left unspecified, each cell will be assigned a value of L (i.e., indicating no missing data). Default is NULL.
readDepth	A Boolean argument indicating whether or not to calculate the mean read depth for each individual from the specified VCF file. Default is FALSE.
nPCs	The number of principal component axes to retain. Default is 4.
outPath	The file path prepended to all output objects.

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:

• thetaW Wu and Watterson's theta, as calculated by calcThetaW

• pwp a matrix of pairwise pi between all samples, as calculated by freqs2pairwisePi

• globalPi global pi in the dataset (the mean of the upper-triangle of pwp)

• pcs the first nPCs principal components, as calculated by doPCA

• het proportion of heterozygous loci in each individual, as calculated by calcHet.

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