impute.snps {snpMatrix} | R Documentation |
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.
impute.snps(rules, snps, subset=NULL)
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 |
A matrix with imputed SNPs as columns. The imputed values are the estimated expected values of each SNP when coded 0, 1 or 2.
Because the imputation is based on a linear model, the imputed value may lie outside the range 0 to 2.
David Clayton david.clayton@cimr.cam.ac.uk
Chapman J.M., Cooper J.D., Todd J.A. and Clayton D.G. (2003) Human Heredity, 56:18-31.
# 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)