calculate_wcFst: Calculate Weir & Cockerham's Fst

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

Calculate Weir & Cockerham's Fst

Description

Calculate Weir & Cockerham's Fst

Usage

snpdata = calculate_wcFst(snpdata, groups=c("Senegal","Gambia"), from="Country")

Arguments

snpdata	SNPdata object
from	the metadata column from which these groups belong to
groups	a vector of string. the differentiation will be estimated between these groups of samples

Value

SNPdata object with an extra field: Fst. This is a list of data frames that contain the result from a specific comparison. Every data frame contains N rows (where N is the number of loci) and the following 7 columns:

1. the chromosome ID

2. the SNPs positions

3. the allele frequency in the first group

4. the allele frequency in the second group

5. the resulting Fst values

6. the p-values associated with the Fst results

7. the p-values corrected for multiple testing using the Benjamini-Hochberg method

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.