17. beta_profile_gene_centered

17.1. Overview

beta_profile_gene_centered generates a transcript-oriented DNA methylation profile across major gene-centered genomic regions.

The profile summarizes average Beta-values across:

upstream intergenic regions
5’ UTR exons
coding exons
first introns
internal introns
last introns
3’ UTR exons
downstream intergenic regions

All regions are oriented from 5’ to 3’ according to transcript strand.

17.2. Input Files

17.2.1. Methylation file

The methylation input must be BED6 or BED6+ with Beta-values in column 5 and strand information in column 6. Compressed input is supported when supported by the CpGtools reader.

The first six columns are expected to represent:

chrom, start, end, name, Beta_value, strand

Example:

chr22   44021512    44021513    cg24055475    0.9231    -
chr13   111568382   111568383   cg06540715    0.1071    +
chr20   44033594    44033595    cg21482942    0.6122    -

17.2.2. Gene model

The reference gene model must be in BED12 format. Strand information is used to determine transcript orientation, UTRs, introns, and upstream/downstream regions.

17.3. Usage

Basic usage:

beta_profile_gene_centered \
    -i test_02.bed6.gz \
    -r hg19.RefSeq.union.bed.gz \
    -o gene_profile

By default, 2,000 bp are included upstream and downstream of each gene.

Useful options include:

-u, --upstream – upstream intergenic length in bp (default: 2000)
-d, --downstream – downstream intergenic length in bp (default: 2000)
--format {png,pdf,both} – plot output format (default: pdf)
--dpi – PNG resolution (default: 300)
--width – plot width in inches (default: 10)
--height – plot height in inches (default: 5)
--no_plot – write the profile table without generating a plot
-o, --out_prefix, --output – output prefix

Display all options with:

beta_profile_gene_centered -h

17.4. Output

For output prefix gene_profile, the command always writes:

gene_profile.gene_centered_profile.tsv – normalized methylation profile

Unless --no_plot is used, it also writes one or more plots:

gene_profile.gene_centered_profile.pdf
gene_profile.gene_centered_profile.png

Use --format both to generate both plot formats.

The profile table contains:

Group – genomic-region category
Relative_position(5'->3') – normalized position within the region
Average_beta – average methylation value