select_genes: Select genes based on variance

In csbl-usp/CEMiTool: Co-expression Modules identification Tool

Select genes based on variance

Description

Select genes based on variance

Usage

select_genes(expr, n_genes, filter_pval = 0.1)

Arguments

expr	A data.frame containing expression values
n_genes	(Optional) Number of genes to be selected
filter_pval	P-value cutoff for gene selection

Value

A vector containing the names of selected genes

Examples

# Get example expression data
data(expr0)
# Filter genes
expr_f <- filter_genes(expr0)
# Check selected genes
expr_f[1:5, 1:5]
# Filter genes and apply variance stabilizing transformation
expr_f2 <- filter_genes(expr0, apply_vst=TRUE)
# Check results
expr_f2[1:5, 1:5]
# Selected genes
selected <- select_genes(expr_f2)
# Get data.frame with only selected genes
expr_s <- expr_f2[selected, ]
# Check results
expr_s[1:5, 1:5]

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.