impute.snps {snpMatrix}R Documentation

Impute snps

Description

Given SNPs stored in an object of class "snpMatrix" or "X.snp.matrix" and a set of imputation equations in as object of class "snp.reg.imputation", this function calculates imputed values.

Usage

impute.snps(rules, snps, subset=NULL)

Arguments

rules The imputation equations; an object of class "snp.reg.imputation"
snps The object of class "snpMatrix" or "X.snp.matrix" containing the observed SNPs
subset A vector describing the subset of subjects to be used. If NULL (default), then use all subjects

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.

Note

Because the imputation is based on a linear model, the imputed value may lie outside the range 0 to 2.

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

References

Chapman J.M., Cooper J.D., Todd J.A. and Clayton D.G. (2003) Human Heredity, 56:18-31.

See Also

snp.imputation

Examples

# Remove 5 SNPs from a datset and derive imputation rules for them
library(snpMatrix)
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 snpMatrix version 1.6.1 Index]