gene_significance {BioNERO}R Documentation

Calculate gene significance for a given group of genes

Description

Calculate gene significance for a given group of genes

Usage

gene_significance(
  exp,
  metadata,
  genes = NULL,
  alpha = 0.05,
  min_cor = 0.2,
  use_abs = TRUE,
  palette = "RdYlBu",
  show_rownames = FALSE,
  continuous_trait = FALSE
)

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.

genes

Character vector of genes to be correlated with traits. If not given, all genes in 'exp' will be considered.

alpha

Significance level. Default is 0.05.

min_cor

Minimum correlation coefficient. Default is 0.2.

use_abs

Logical indicating whether to filter by correlation using absolute value or not. If TRUE, a min_cor of say 0.2 would keep all correlations above 0.2 and below -0.2. Default is TRUE.

palette

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

show_rownames

Logical indicating whether to show row names or not. Default is FALSE.

continuous_trait

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

Value

A heatmap of gene significance (GS) and a list containing:

See Also

corPvalueStudent RColorBrewer

Examples

data(filt.se)
gs <- gene_significance(filt.se)

[Package BioNERO version 1.2.0 Index]