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Last data update: 2014.03.03

R: Create a nongeno Object

nongeno

R Documentation

Create a nongeno Object

Description

Creates an object of class nongeno containing a non-genotype design matrix, the type of kernel to generate, and the weights to be used to create the kernel matrix. This function is used to simplify the input structure of the call to KITdesign.

Usage

nongeno(mat, kernel = "linear", weights = NULL)

Arguments

`mat`	Design matrix. Missing values must be coded as NA.
`kernel`	Type of kernel. Must be one of 'interactive', 'linear', 'quadratic'. For linear kernel, the constant is taken to be zero; for quadratic kernel, it is one.
`weights`	Weights, if any, to be used in generating kernel. Object can be a vector or matrix. If vector, weights is converted to a diagonal matrix.

Value

Returns an object of class nongeno containing the design matrix, the weights to be used in generating the kernel, and the type of kernel to be generated.

Author(s)

Shannon T. Holloway

Examples

  ngdata <- matrix(rnorm(40),ncol=4L)

  nongeno(mat = ngdata, kernel = "linear", weights = NULL)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FastKM)
Loading required package: rARPACK

FastKM was developed in support of IMPACT, a comprehensive research
program that aims to improve the health and longevity of people by
improving the clinical trial process. To learn more about our 
research and available software visit www.impact.unc.edu. 


> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FastKM/nongeno.Rd_%03d_medium.png", width=480, height=480)
> ### Name: nongeno
> ### Title: Create a nongeno Object
> ### Aliases: nongeno
> 
> ### ** Examples
> 
>   ngdata <- matrix(rnorm(40),ncol=4L)
> 
>   nongeno(mat = ngdata, kernel = "linear", weights = NULL)
An object of class "nongeno"
Slot "mat":
            [,1]       [,2]        [,3]       [,4]
 [1,]  1.2221855 -1.7997989 -0.39625893  1.6673549
 [2,]  2.0666508  0.1631835  0.37269109  0.4700132
 [3,]  0.5619514 -0.6573744 -0.82086947  0.3145496
 [4,]  0.5713317  0.7895786  1.25020560 -0.8770039
 [5,] -0.3954048  0.5205967 -0.53597046 -1.8155924
 [6,] -0.7858411  0.2011017  1.52311433  1.1208910
 [7,] -0.6737329  1.3362339  0.67724527  0.1735102
 [8,]  0.7935315  2.0346218 -0.07134176 -0.5942901
 [9,] -1.4061323 -1.1687705 -0.16533066 -0.2567213
[10,]  2.3098466 -1.2993260  0.25014042 -1.4988172

Slot "kernel":
[1] "linear"

Slot "weights":
     [,1]
[1,]    1
[2,]    1
[3,]    1
[4,]    1

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>