R: F-statistics (fixation indices)

snpgdsFst {SNPRelate}

R Documentation

F-statistics (fixation indices)

Description

Calculate relatedness measures F-statistics (also known as fixation indices) for given populations

Usage

snpgdsFst(gdsobj, population, method=c("W&C84", "W&H02"), sample.id=NULL,
    snp.id=NULL, autosome.only=TRUE, remove.monosnp=TRUE, maf=NaN,
    missing.rate=NaN, with.id=FALSE, verbose=TRUE)

Arguments

`gdsobj`	an object of class `SNPGDSFileClass`, a SNP GDS file
`population`	a factor, indicating population information for each individual
`method`	`"W&C84"` – Fst estimator in Weir & Cockerham 1984 (by default), `"W&H02"` – relative beta estimator in Weir & Hill 2002, see details
`sample.id`	a vector of sample id specifying selected samples; if NULL, all samples are used
`snp.id`	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
`autosome.only`	if `TRUE`, use autosomal SNPs only; if it is a numeric or character value, keep SNPs according to the specified chromosome
`remove.monosnp`	if TRUE, remove monomorphic SNPs
`maf`	to use the SNPs with ">= maf" only; if NaN, no MAF threshold
`missing.rate`	to use the SNPs with "<= missing.rate" only; if NaN, no missing threshold
`with.id`	if `TRUE`, the returned value with `sample.id` and `sample.id`
`verbose`	if `TRUE`, show information

Details

The minor allele frequency and missing rate for each SNP passed in snp.id are calculated over all the samples in sample.id.

The "W&H02" option implements the calculation in Buckleton et. al. 2016.

Value

Return a list:

`sample.id`	the sample ids used in the analysis
`snp.id`	the SNP ids used in the analysis
`Fst`	weighted Fst estimate
`MeanFst`	the average of Fst estimates across SNPs
`FstSNP`	a vector of Fst for each SNP
`Beta`	Beta matrix

Author(s)

Xiuwen Zheng

References

Weir, BS. & Cockerham, CC. Estimating F-statistics for the analysis of population structure. (1984).

Weir, BS. & Hill, WG. Estimating F-statistics. Annual review of genetics 36, 721-50 (2002).

Population-specific FST values for forensic STR markers: A worldwide survey. Buckleton J, Curran J, Goudet J, Taylor D, Thiery A, Weir BS. Forensic Sci Int Genet. 2016 Jul;23:91-100. doi: 10.1016/j.fsigen.2016.03.004.

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

group <- as.factor(read.gdsn(index.gdsn(
    genofile, "sample.annot/pop.group")))

# Fst estimation
v <- snpgdsFst(genofile, population=group, method="W&C84")
v$Fst
v$MeanFst
summary(v$FstSNP)

# or
v <- snpgdsFst(genofile, population=group, method="W&H02")
v$Fst
v$MeanFst
v$Beta
summary(v$FstSNP)

# close the genotype file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]