# Optimising the Definition of Expressed Regions

## Documentation for package ‘ODER’ version 1.6.0

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

## Help Pages

add_expressed_genes | Adding the nearest expressed genes
annotatERs | Connects ERs to genes using junction data, then classifies ERs into "exonic", "intronic", "intergenic", or a combination of these categories
file_cache | Cache a file if it is not found locally
get_chr_info | Get information from UCSC about the chromosomes passed in
get_count_matrix | Generate the count matrix
get_coverage | Obtain the mean coverage across multiple BigWig files
get_ers | Define sets of ERs
get_ers_delta | Obtain set of non-overlapping exons
get_exons | Obtain set of non-overlapping exons
get_opt_ers | Obtain set of non-overlapping exons
get_strand_ers | Define sets of ERs
gtex_SRP012682_SRX222703_lung_auc_1 | An example AUC value
gtex_SRP012682_SRX222703_lung_coverage_1 | An example object containing coverage
gtex_SRP012682_SRX222703_lung_erdelta_1 | An example set of ER deltas
gtex_SRP012682_SRX222703_lung_ers_1 | An example set of Expressed Regions
lung_junc_21_22 | Junction data of chromosomes 21 and 22 from a lung tissue sample
ODER | ODER: Optimising the Definition of Expressed Regions
plot_ers | Plot Expressed regions
pseudogene | Different transcript biotypes that count as pseudogene
refine_ERs | Refines the ERs start and end points
tissue_options | The different tissues that can be filtered on for gene expression