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:

- filtered_corandpFiltered matrix of correlation and p-values

- raw_GSRaw matrix of gene significances

### See Also

`corPvalueStudent` `RColorBrewer`

### Examples

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

[Package BioNERO version 1.0.4 Index]