filter_genes {CEMiTool} | R Documentation

## Filter a gene expression data.frame

### Description

Filter a gene expression data.frame

### Usage

    filter_genes(expr, pct = 0.75, apply_vst = FALSE)

### Arguments

`expr` | A data.frame containing expression data
`pct` | Percentage of most expressed genes to keep.
`apply_vst` | Logical. If TRUE, will apply variance stabilizing transform before filtering data.

### Details

This function takes a gene expression data.frame and applies a percentage filter (keeps the `pct`) most expressed genes). If `apply_vst` is TRUE, a variance stabilizing transformation is applied on gene expression values as long as mean and variance values have a Spearman's rho of over 0.5. This transformation is intended to remove this dependence between the parameters. One should then apply the `select_genes` function to get significant genes.

### Value

A data.frame containing filtered expression data

### 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]

[Package CEMiTool version 1.16.0 Index]