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 1.8.0 Index]