checkMetadata: checkMetadata

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

checkMetadata

Description

Validate and extract non-empty annotation fields from a GTF file.

Usage

checkMetadata(gtfPath, typeFilter)

Arguments

gtfPath	Character. Path to the directory or file location of the GTF file.
typeFilter	Character. The feature type to filter on (e.g., "gene", "exon").

Details

This function imports a GTF file, filters entries by a specified feature type, and identifies metadata columns that contain at least one non-missing value.

1. Imports the GTF into a data frame via "rtracklayer::import()".

2. Filters rows by "type" == typeFilter.

3. Tests each column for all-NA or empty-string entries.

4. Returns names of columns with at least one non-missing, non-empty value.

Value

Character vector of column names in the GTF annotation that are not entirely NA or empty.

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.