prep_limma: Prepare limma-voom DEG data for plotting

In TransProR: Analysis and Visualization of Multi-Omics Data

Prepare limma-voom DEG data for plotting

Description

This function reads a limma-voom DEG data frame from an RDS file, filters it using deg_filter function, adjusts the logFC to absolute values, adds a pseudo-count to P.Value, and transforms P.Value for plotting. The final data frame is returned and optionally saved to a new RDS file.

Usage

prep_limma(input_path, output_name = NULL)

Arguments

input_path	Path to the RDS file containing the limma-voom DEG data frame.
output_name	Name for the processed data frame, also used as the RDS file name.

Value

A data frame with processed limma-voom DEG data.

Examples

limma_file <- system.file("extdata",
                          "DEG_limma_voom_test.rds",
                          package = "TransProR")
limma <- prep_limma(limma_file)

TransProR documentation built on April 4, 2025, 3:16 a.m.