A class defining a list "rules" for imputation of
SNPs. Rules are estimated population
haplotype probabilities for a target SNP and one or more predictor 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.
hap.probs
A numerical array containing estimated
probabilities for haplotypes of the SNP to be imputed and all the
predictor SNPs
If any target SNP is monomorphic, the corresponding rule is
returned as NULL. An object of class ImputationRules
has an attribute, Max.predictors, which gives the maximum
number of predictors used for any imputation.
Methods
show
signature(object = "ImputationRules"): prints
an abreviated listing of the rules
summary
signature(object = "ImputationRules"):
returns a table which shows the distribution of r-squared values
achieved against the number of snps used for imputation
plot
signature(x="ImputationRules", y="missing"):
plots the distribution of r-squared values as a stacked bar chart
[]
signature(x = "ImputationRules", i = "ANY"): subset
operations
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(snpStats)
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/snpStats/ImputationRules-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ImputationRules-class
> ### Title: Class "ImputationRules"
> ### Aliases: ImputationRules-class show,ImputationRules-method
> ### summary,ImputationRules-method plot,ImputationRules,missing-method
> ### [,ImputationRules,ANY,missing,missing-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("ImputationRules")
Class "ImputationRules" [package "snpStats"]
Slots:
Name: .Data
Class: list
Extends:
Class "list", from data part
Class "vector", by class "list", distance 2
>
>
>
>
>
> dev.off()
null device
1
>