snp.reg.imputation-class {snpMatrix}R Documentation

Class "snp.reg.imputation"

Description

A class defining a list of regression equations, or "rules", for imputation of SNPs

Objects from the Class

Objects are lists of rules. Rules are named list elements each describing imputation of a SNP by a linear regression equation. Each element is itself a list with the following elements:

maf
The minor allele frequency of the imputed SNP
r.squared
The squared Pearson correlation coefficient between observed and predicted SNP duration derivation of the rule.
snps
The names of the SNPs to be included in the regression.
coefficients
A numeric array containing the regression equation intercept followed by the regression coefficients for the SNPs listed in snps.

If any target SNP is monomorphic, the corresponding rule is returned as NULL.

Methods

show
signature(object = "snp.reg.imputation"): prints an abreviated listing of the rules
summary
signature(object = "snp.reg.imputation"): returns a table which shows the distribution of r-squared values achieved against the number of snps used for imputation
plot
signature(x="snp.reg.imputation", y="missing"): plots the distribution of r-squared values as a stacked bar chart
[]
signature(x = "snp.reg.imputation", i = "ANY"): subset operations

Author(s)

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

See Also

snp.imputation, impute.snps, single.snp.tests

Examples

showClass("snp.reg.imputation")

[Package snpMatrix version 1.6.1 Index]