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 1.8.0 Index]