impute.snps {snpStats} | R Documentation

## Impute snps

### Description

Given SNPs stored in an object of class `"SnpMatrix"` or `"XSnpMatrix"` and a set of imputation rules in an object of class `"ImputationRules"`, this function calculates imputed values.

### Usage

    impute.snps(rules, snps, subset = NULL, as.numeric = TRUE)

### Arguments

`rules` | The imputation rules; an object of class `"ImputationRules"`
`snps` | The object of class `"SnpMatrix"` or `"XSnpMatrix"` containing the observed SNPs
`subset` | A vector describing the subset of subjects to be used. If `NULL` (default), then use all subjects
`as.numeric` | If `TRUE`, the output is a numeric matrix containing posterior expectations of the imputed SNPs. Otherwise the output matrix is of the same class as `snps` and contains uncertain genotype calls

### Value

A matrix with imputed SNPs as columns. The imputed values are the estimated expected values of each SNP when coded 0, 1 or 2.

### Author(s)

David Clayton dc208@cam.ac.uk

### References

Wallace, C. et al. (2010) Nature Genetics, 42:68-71

### See Also

`snp.imputation`

### Examples

    # Remove 5 SNPs from a datset and derive imputation rules for them
    data(for.exercise)
    sel <- c(20, 1000, 2000, 3000, 5000)
    to.impute <- snps.10[,sel]
    impute.from <- snps.10[,-sel]
    pos.to <- snp.support$position[sel]
    pos.fr <- snp.support$position[-sel]
    imp <- snp.imputation(impute.from, to.impute, pos.fr, pos.to)
    # Now calculate the imputed values
    imputed <- impute.snps(imp, impute.from)

[Package snpStats version 1.42.0 Index]