filter_expr {CEMiTool} | R Documentation

## Filter gene expression table

### Description

Filter gene expression table

### Usage

    filter_expr(cem, ...)

    ## S4 method for signature 'CEMiTool'
    filter_expr(cem, filter_pval = 0.1, n_genes,
      pct = 0.75, apply_vst = FALSE)

### Arguments

`cem` | Object of class `CEMiTool`.
`...` | Optional parameters.
`filter_pval` | P-value cutoff for gene selection.
`n_genes` | Number of genes to be selected.
`pct` | Percentage of most expressed genes to keep (before variance filter).
`apply_vst` | Logical. If TRUE, will apply variance stabilizing transform before filtering data.

### Value

Object of class `CEMiTool` with selected genes

### Examples

    # Get example expression data
    data(expr0)
    # Initialize CEMiTool object with expression
    cem <- new_cem(expr0)
    # Filter genes
    cem1 <- filter_expr(cem)
    # Check selected genes
    head(expr_data(cem1))
    # Filter genes and apply variance stabilizing transformation
    cem2 <- filter_expr(cem, apply_vst=TRUE)
    # Check results
    head(expr_data(cem2))

[Package CEMiTool version 1.4.2 Index]