pleio.demo: Demonstration dataset for pleiotropy tests with a mixture of...

In pleio: Pleiotropy Test for Multiple Traits on a Genetic Marker

Description

A simulated dataset with 3 y variables simulated from multivariate normal with common correlation structure, correlation of 0.5. The traits are (1) gaussian, (2) binomial, and (3) ordinal. Genotypes were simulated based on minor allele frequency of 0.2, and assume that the 3 traits are not asssociated with dose of minor allele (all 3 betas = 0).

Usage

data("pleio.demo")

Format

y is a data.frame with 500 observations and 3 traits, whose distribution families are gaussian, binomial, and ordinal, respectively; x is a matrix of 5 covariates, geno is a single SNP of dosage of a minor allele simulated from frequency of 0.2.

Examples

data(pleio.demo)
str(y)
table(geno)
x[1:5,]

Example output

Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Matrix
 num [1:500, 1:3] 1.323 1.552 1.067 1.598 -0.685 ...
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:3] "y.gaus" "y.bin" "y.ord"
geno
  0   1   2 
320 154  26 
           var1       var2        var3        var4       var5
[1,] -1.5717502  1.8026828 -0.04479937 -1.92511172  1.3448986
[2,] -0.9178921 -0.1813772  0.24515112 -0.84067111  0.3347633
[3,] -0.1959975 -0.2964851 -1.32939952 -0.08900092 -0.6227293
[4,]  0.1258191 -0.2039832  1.58518754 -0.26349043 -1.5810298
[5,]  1.2446132  1.5843587  0.91316989  1.60291419  2.3343767

pleio documentation built on May 2, 2019, 7:27 a.m.