snp.imputation {snpMatrix} | R Documentation |
Given two set of SNPs typed in the same subjects, this function calculates regression equations which can be used to impute one set from the other in a subsequent sample.
snp.imputation(X, Y, pos.X, pos.Y, phase=FALSE, try = 50, r2.stop = 0.9, max.X = 4)
X |
An object of class "snpMatrix" or
"X.snp.matrix" containing observations
of the SNPs to be used for imputation ("regressor SNPs") |
Y |
An object of same class as X containing observations
of the SNPs to be imputed in a future sample ("target SNPs") |
pos.X |
The positions of the regressor SNPs |
pos.Y |
The positions of the target SNPs |
phase |
See "Details" below |
try |
The number of potential regressor SNPs to be
considered in the stepwise regression procedure around each target
SNP . The nearest try regressor SNPs to each target SNP
will be considered |
r2.stop |
The value of R^2 at which to stop entering new variables in the step-wise regression. If set to 1.0 or greater, the AIC will be used |
max.X |
The maximum number of regressor SNPs to be used for each imputation |
The routine carries out a series of step-wise regression analyses in
which each Y SNP is regressed on the nearest try
regressor SNPs. If
phase
is TRUE
, the regressions are calculated at the
chromosome (haplotype) level, variances being simply p(1-p) and
covariances estimated
using the same algorithm used in ld.snp
. Otherwise, the
analysis is carried out at the diplotype level based on
conventional variance and covariance estimates using the
"all.obs"
missing value treatment (see cov
).
An object of class
"snp.reg.imputation"
.
The phase=TRUE
option is not yet implemented
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.
snp.reg.imputation-class
, ld.snp
# 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)