getDegMerged: getDegMerged
In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

getDegMerged

R Documentation

getDegMerged

Description

Merge multiple DEG result CSVs with GTF annotations into a single data frame.

Usage

getDegMerged(path, gtfPath, columns, collapseName, typeFilter, selectUpDown)

Arguments

`path`	Character. Directory containing DEG result CSV files.
`gtfPath`	Character. Path to the GTF annotation file.
`columns`	Character vector. Names of annotation columns to include from the GTF.
`collapseName`	Logical. If TRUE, strip method/model prefixes from file names when prefixing columns.
`typeFilter`	Character. GTF feature type to filter (e.g., "gene" or "transcript").
`selectUpDown`	Logical. If TRUE, only include IDs with "diffExp" == UP or DOWN.

Details

This function reads all CSV files in a directory, validates presence of required columns ("ID", and optionally "diffExp"), filters for up/down regulated genes if requested, extracts annotation fields from a GTF, and returns a merged table of selected annotation columns alongside all DEG metrics (with optional file-based column prefixes).