metaGE.test {metaGE}

Meta-analysis test for Genotype x Environment interactions: Contrast or Regression.

Description

The function metaGE.test compute meta-analysis contrast or regression test.

Usage

metaGE.test(
  Data,
  MatCorr,
  Incidence = NULL,
  Contrast = NULL,
  Covariate = NULL,
  EnvName = NULL,
  NA.omit = TRUE,
  DropZScores = FALSE
)

Arguments

Data

A dataset containing the estimated marker effect and its associated pvalue of each marker (in rows) in each environment (in columns), as obtained from metaGE.collect.

MatCorr

The inter-environment correlation matrix. It can be compute by the metaGE.cor function.

Incidence

A matrix of incidence, as obtained from metaGE.incidence or a list of such matrix.

Contrast

A matrix of contrast, or a list of such matrix.

Covariate

A dataset containing the values of one or more covariates (in columns) in each environment (in rows).

EnvName

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

NA.omit

A boolean specifying whether the markers with some NA values should be removed from the test procedure. (TRUE by default)

DropZScores

A boolean specifying whether the Zscores should be dropped from the dataset or not. (FALSE by default)

Details

If Incidence is provided, the function will perform all the corresponding tests of contrast. If Covariate is provided, the function will perform all the corresponding meta-regression tests. The Contrast can be NULL, in this case the identity matrix is used.

Value

The dataset Data with supplementary columns containing the Pvalue of each test performed.

Examples

require(dplyr)

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

#' # Compute the inter-environment correlation matrix
matCorr <- metaGE.cor(metaData, Threshold = 0.8)

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

# Perform the contrast test
ContrastDF <- metaGE.test(metaData, matCorr,Incidence = Incidence.Water, Contrast = NULL)
head(ContrastDF %>% select(CHR, POS, MARKER, PVALUE.Contrast1))

#### Regression test
RegressionDF <- metaGE.test(metaData,matCorr, Covariate = envDesc[,c(1,5)],EnvName = "ShortName" )
head(RegressionDF %>% select(CHR, POS, MARKER, PVALUE.Tnight.mean))