metaGE.heatmap: Draw the heatmap to see markers effects across environments.

In metaGE: Meta-Analysis for Detecting Genotype x Environment Associations

Draw the heatmap to see markers effects across environments.

Description

The function metaGE.heatmap displays the heatmap of the zscores, the estimated marker effects or the pvalues of each markers (in rows) in each environments (in columns).

Usage

metaGE.heatmap(
  Data,
  Prefix = "Z.",
  EnvGroups = NULL,
  QTLsVarName = NULL,
  RowOrder = TRUE,
  ColOrder = TRUE,
  ShowDendrogram = FALSE,
  Colors = c("red", "black", "green"),
  Main = ""
)

Arguments

Data	A dataset containing the zscores, the effects or the pvalues of each marker (in rows) in each environment (in columns), as obtained from metaGE.fit().
Prefix	The prefix of the score to display in the heatmap: "Z." for the zscores, "EFFECT." for the effects and "PVAL." for the pvalues.("Z." by default)
EnvGroups	A dataset containing the names of the environments (in the first column) and the groups to which the environments belong (in the second column). (optional)
QTLsVarName	The name of the column indicating to which QTL the marker belongs. (optional)
RowOrder	A boolean specifying whether to reorder the markers or not. (TRUE by default)
ColOrder	A boolean specifying whether to reorder the environments or not. (TRUE by default)
ShowDendrogram	A boolean specifying whether to show the clustering of the rows and/or the columns. (FALSE by default)
Colors	A vector of three colors corresponding to the color scale of the Heatmap.(optional)
Main	The main to display.(optional)

Value

The heatmap

Examples

require(dplyr)
# Import the data
data("metaData")

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

# Fit the Fixed Effect model
FeDF <- metaGE.fit(metaData, matCorr, Method = "Fe")

# Control the FDR (here Benjamini-Hochberg)
Alpha <- 0.05
Signif <-  FeDF$PVALUE %>% p.adjust(method = "BH") %>% `<`(Alpha) %>% which

# Draw the z-scores heatmap of the significant markers
heatmap <- metaGE.heatmap(Data = FeDF[Signif,],
                         Prefix = "Z.")
                        

metaGE documentation built on April 3, 2025, 8:48 p.m.