MangroveBetas: The MangroveBetas class

In Mangrove: Risk Prediction on Trees

Description

Functions to read in and use MangroveBetas objects

Usage

readBetas(betafile,header=TRUE)

## S3 method for class 'MangroveBetas'
print(x, ...)
## S3 method for class 'MangroveBetas'
summary(object, ...)
## S3 method for class 'MangroveBetas'
plot(x, ...)

Arguments

betafile	The location of a beta file to read in
header	Logical. Indicates whether the betafile above has a header.
x	A MangroveBetas object
object	A MangroveBetas object
...	Additional arguments to be passed to downstream methods.

Details

A MangroveBetas object is used to hold the risk alleles, beta values and frequencies for a set of genetic variants used to predict a quantitative trait. You can read a beta file from disk using readBetas.

The format of the beta file is a text file with 4 columns. The first should be the variant ID, the second the risk allele, the third the additive beta value and the fourth the frequency.

The print method shows the data that the object holds. The summary method gives some measures of how predictive the variants are, including the variance explained by the variants in the object. The plot method show the cumulative variance explained as the variants are added in one-at-a-time (in order of most-to-least variance explained).

See vignette("Mangrove") for an example of a beta file, and usage of a beta object.

Value

An object of class MangroveBetas for readBetas. Nothing is returned for the methods.

See Also

MangroveContPreds for performing quantitative trait prediction using this object.

Examples

data(exampleBetas)
summary(exampleBetas)
plot(exampleBetas)

Mangrove documentation built on May 1, 2019, 9:10 p.m.