gene_significance: Calculate gene significance for a given group of genes

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Calculate gene significance for a given group of genes

Description

Calculate gene significance for a given group of genes

Usage

gene_significance(
  exp,
  metadata,
  metadata_cols = NULL,
  genes = NULL,
  alpha = 0.05,
  cor_method = "pearson",
  min_cor = 0.2,
  use_abs = TRUE
)

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.
metadata_cols	A vector (either numeric or character) indicating which columns should be extracted from column metadata if exp is a 'SummarizedExperiment' object. The vector can contain column indices (numeric) or column names (character). By default, all columns are used.
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.
cor_method	Method to calculate correlation. One of 'pearson', 'spearman' or 'kendall'. Default is 'spearman'.
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.

Value

A data frame with correlation and correlation p-values for each pair of gene and trait, with the following variables:

gene

Factor, gene ID.

trait

Factor, trait name. Each trait corresponds to a variable of the sample metadata (if numeric) or levels of a variable (if categorical).

cor

Numeric, correlation.

pvalue

Numeric, correlation P-values.

group

Character, name of the metadata variable.

Author(s)

Fabricio Almeida-Silva

Examples

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

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.