Remove Genes with Low Expression

This function filters out genes with expression values below a specified quantile threshold in at least a minimum number of replicates per condition.

Usage

remove_low_expression(
  dds,
  group_by,
  quantile = 0.05,
  save_plot = TRUE,
  save_dir = getwd()
)

Arguments

dds

A DESeq2 object containing the gene expression data

group_by

Column name in colData(dds) to use for defining conditions. Default is "Group1"

quantile

Quantile threshold for filtering. Default is 0.05 (lowest 5%)

save_plot

Logical. If TRUE, saves the expression distribution plot. Default is TRUE

save_dir

Directory to save the plot. Default is the current working directory

Value

A filtered DESeq2 object with low-expression genes removed

Examples

if (FALSE) { # \dontrun{
# Remove bottom 5% of genes
dds_filtered <- remove_low_expression(dds, quantile = 0.05)

# Remove bottom 10% of genes and save plot
dds_filtered <- remove_low_expression(dds, quantile = 0.1, save_plot = TRUE)
} # }