gene_significance {BioNERO} | R Documentation |
Calculate gene significance for a given group of genes
gene_significance( exp, metadata, genes = NULL, alpha = 0.05, min_cor = 0.2, use_abs = TRUE, palette = "RdYlBu", show_rownames = FALSE, continuous_trait = FALSE )
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 |
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. |
A heatmap of gene significance (GS) and a list containing:
filtered_corandpFiltered matrix of correlation and p-values
raw_GSRaw matrix of gene significances
data(filt.se) gs <- gene_significance(filt.se)