module_trait_cor {BioNERO}R Documentation

Correlate module eigengenes to trait

Description

Correlate module eigengenes to trait

Usage

module_trait_cor(
  exp,
  metadata,
  MEs,
  cor_method = "spearman",
  transpose = FALSE,
  palette = "RdYlBu",
  continuous_trait = FALSE,
  cex.lab.x = 0.6,
  cex.lab.y = 0.6,
  cex.text = 0.6
)

Arguments

exp

A gene expression data frame with genes in row names and samples in column names or a 'SummarizedExperiment' object.

metadata

A data frame containing sample names in row names and sample annotation in the first column. Ignored if 'exp' is a 'SummarizedExperiment' object, since the function will extract colData.

MEs

Module eigengenes. It is the 2nd element of the result list generated by the function exp2gcn.

cor_method

Method to calculate correlation. One of 'pearson', 'spearman' or 'kendall'. Default is 'spearman'.

transpose

Logical indicating whether to transpose the heatmap of not. Default is FALSE.

palette

RColorBrewer's color palette to use. Default is "RdYlBu", a palette ranging from blue to red.

continuous_trait

Logical indicating if trait is a continuous variable. Default is FALSE.

cex.lab.x

Font size for x axis labels. Default: 0.6.

cex.lab.y

Font size for y axis labels. Default: 0.6.

cex.text

Font size for numbers inside matrix. Default: 0.6.

Details

Significance levels: 1 asterisk: significant at alpha = 0.05. 2 asterisks: significant at alpha = 0.01. 3 asterisks: significant at alpha = 0.001. no asterisk: not significant.

Value

A data frame with correlation and correlation p-values for each pair of ME and trait along with a heatmap.

Author(s)

Fabricio Almeida-Silva

See Also

corPvalueStudent,labeledHeatmap,blueWhiteRed

Examples

data(filt.se)
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
module_trait_cor(filt.se, MEs=gcn$MEs)

[Package BioNERO version 1.2.0 Index]