# A package to produce metagene plots

## Documentation for package ‘metagene2’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as_is_region_order | Returns an "as-is" ordering of regions.
Bam_Handler | A class to manage BAM files.
coverage_order | Determines ordering of regions as a function of coverage.
get_demo_bam_files | Get BAM filenames for demo
get_demo_design | Get a demo design object
get_demo_metagene | Get a demo metagene object
get_demo_regions | Get demo regions
get_demo_region_filenames | Get regions filenames for demo
get_demo_rna_bam_files | Get BAM filenames for demo
get_demo_rna_regions | Get demo regions
metagene2 | A class to manage metagene analysis.
metagene2_heatmap | Plots a heatmap of coverages from a metagene2 object.
plot_metagene | Produce a metagene plot