metaGE.incidence {metaGE}

Create the matrix of incidence.

Description

The function metaGE.incidence convert categorical variable describing the environments into a matrix of dummy variables with in rows the levels of the variables and in columns the environment.

Usage

metaGE.incidence(VarName, Covariate, EnvName, Data, AtLeast = 1)

Arguments

VarName

The name of the column containing the categorical variable in the Covariate dataset.

Covariate

A dataset containing categorical variables (in columns) describing the environments (in rows).

EnvName

The name of the column containing the names of the environment in the Covariate dataset.

Data

A dataset containing the effects and pvalues of each marker (in rows) in each environment (in columns), as obtained from metaGE.collect.

AtLeast

A numeric value indicating the minimum number of environments must belong to each level (equals 1 by default).

Details

The names of the environment must be the same as used in the Data dataset.

Value

A binary matrix containing indicator variables with in rows the levels of the variables and in columns the environment.

Examples

# Import the data
data("metaData")
data("envDesc")

# Build the matrix of incidence
(Incidence.Temp <- metaGE.incidence(VarName = "Temp",Covariate = envDesc,
                                    EnvName = "ShortName", Data = metaData))