MangroveRiskPreds: The MangroveRiskPreds class

In Mangrove: Risk Prediction on Trees

Description

Methods to generate, summarise and apply MangroveRiskPreds objects

Usage

calcORs(ped,ORs)
applyORs(riskpred,K)

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

Arguments

ped	A MangrovePed object
ORs	A MangroveORs object
riskpred	A MangroveRiskPreds object
object	A MangroveRiskPreds object
x	A MangroveRiskPreds object
K	The prevalence of the disease being predicted.
...	Arguments to be passed on to downstream methods.

Details

MangroveRiskPreds objects are used to hold risk predictions for a number of individuals. This object contains the odds ratio for each individual of developing the disease, relative to the population average. You can generate risk predictions from a pedigree object and some per-variant odds ratios using calcORs, and you can use these to calculate posterior probabilities of developing the disease given a prevalence using applyORs.

The print method writes the odds ratio for each individual to screen. The summary method gives some quantile information, and the plot method prints a histogram of log odds ratios, which should be approximately normal.

Value

calcORs returns a MangroveRiskPreds object, applyORs returns a numeric vector containing posterior probabilities. The methods do not return anything.

See Also

MangroveTree for doing risk prediction for a whole family. MangroveContPreds for doing quantitative trait prediction.

Examples

data(ccped)
data(exampleORs)
ccors <- calcORs(ccped,exampleORs)

summary(ccors)
plot(ccors)

ccposts <- applyORs(ccors,0.02)

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