define_boundaries: Define the genomic region spanning all the feature types of...

In UW-GAC/genetable: Functions to Build a Gene Definitions Table in the GAC Database

Description

This function processes a filtered gencode tibble (such as returned from filter_gencode()) to define the genomic region that spans all the features of interest.

Usage

define_boundaries(filtered_gtf, grouping = "gene_id")

Arguments

filtered_gtf	The filtered gencode tibble
grouping	The feature type of interest. Must be a field of the filtered_gtf tibble (e.g., feature Default = "gene_id".

Details

NOTE: for now, this works for grouping on gene_id. I may generalize later if we want to group on other features.

Value

A tibble containing the regions of interest. Variables in this tibble include: - chr - chromosome in genome build GRCh37/hg19 - strand - DNA strand. values +,- - gene_id - gene identifier with ENSG prefix - gene_name - Gene name - agg_start - lower bound of genic unit - agg_end - upper bound of genic unit - source - comma seprated lists values of annotation sources of transcripts in a genic unit - transcript_type - comma seprated values of biotypes of transcripts in a genic unit - merge_count - number of transcripts merged in the genic unit - agg_size - length of the genic unit derived as a difference of agg_end agg_start

Examples

## Not run: 
define_boundaries(filtered_gtf, feature = "gene_id")

## End(Not run)

UW-GAC/genetable documentation built on May 5, 2019, 11:08 p.m.