SNPRelate (version 1.6.4)

snpgdsFst: 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&H02", "W&C84"), 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&H02" -- relative beta estimator in Weir&Hill 2002, "W&C84" -- Fst estimator in Weir&Cockerham 1984

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 "

with.id

if TRUE, the returned value with sample.id and sample.id

verbose

if TRUE, show information

Value

Return a list:

sample.id

the sample ids used in the analysis

snp.id

the SNP ids used in the analysis

Fst

Fst estimator

Beta

Beta matrix

Details

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

References

Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. (1984).

Weir, B. S. & Hill, W. G. Estimating F-statistics. Annual review of genetics 36, 721-50 (2002).

Examples

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

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

# Fst estimation
snpgdsFst(genofile, population=group, method="W&H02")

# or
snpgdsFst(genofile, population=group, method="W&C84")


# close the genotype file
snpgdsClose(genofile)