ContrastStatTest.NA {metaGE}

Compute the statistic of the contrast test in presence of missing values

Description

The function ContrastStatTest compute the statistic of the contrast test.

Usage

ContrastStatTest.NA(
  Incidence,
  Contrast = NULL,
  Zmat,
  MatCorr,
  Data,
  Configs.list,
  IncidenceName
)

Arguments

Incidence

A matrix of incidence, as obtained from metaGE.incidence.

Contrast

A matrix of contrast, if NULL the identity matrix is used. (NULL by default)

Zmat

A matrix containing the Zscores of all markers (in rows) in each environment (in columns).

MatCorr

The inter-environments correlation matrix. Can be computed using MetaGE.cor.

Data

A dataset containing the effect, the pvalues and the na configuration for all marker

Configs.list

A vector containing the NA configurations present in the dataset

IncidenceName

The name of the incidence.

Value

A dataset of two columns containing the pvalue of the test of contrast and the minimum number of environment per group of all markers.