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 1.28.0 Index]