Generate Reduced GTF Annotations — create_reduced

This function creates a simplified GTF-style data frame by selecting key columns and adding annotation type and transcript source. Data must be pre-loaded using load_annotation() followed by create_GTF_df() and / or add_UTR(), create_full_GTF(), or create_reduced_GTF().

create_reduced_GTF(input)

Arguments

input: A data frame containing genomic data with the following columns: - `chr`: Chromosome identifier - `start`: Start position of the annotation - `end`: End position of the annotation - `strand`: Strand information ('+' or '-') - `transcript_name`: Name of the associated transcript - `transcript_id`: Unique identifier for the transcript - `gene_name`: Name of the associated gene - `gene_id`: Unique identifier for the gene - `annotationType`: Type of annotation (e.g., 'EXON', 'TRANSCRIPT') - `source`: Source of the transcript - `gene_id`: Unique identifier for the gene - `gene_name`: Name of the associated gene - `transcript_name`: Name of the associated transcript - `transcript_id`: Unique identifier for the transcript

Value

A data frame containing the following columns: - `chr`: Chromosome identifier - `start`: Start position of the annotation - `end`: End position of the annotation - `strand`: Strand information - `transcript_name`: Transcript name - `transcript_id`: Transcript ID - `gene_name`: Gene name - `gene_id`: Gene ID - `annotationType`: Annotation type - `transcriptType`: Transcript source

Examples


# Run the function
reduced_gtf_data <- create_reduced_GTF(input_data)
#> Error: object 'input_data' not found