4. CpG_density_gene_centered

4.1. Overview

CpG_density_gene_centered generates a transcript-oriented CpG density profile across three gene-centered regions:

Each region is normalized into bins by CpGtools’ density calculation (currently 100 bins per region), producing a 5’-to-3’ metagene profile.

Upstream and downstream extensions are constrained by neighboring genes, so the actual flanking regions may be shorter than the requested maximum.

The CpG input must be BED3 or BED3+ and contain genomic CpG positions.

Example:

chr1    10847    10848
chr1    10849    10850
chr1    15864    15865

Compressed input is supported by the CpGtools reader.

The reference gene model must be BED6+ and include strand information so that TSS, TES, upstream, and downstream directions can be determined.

Basic usage:

CpG_density_gene_centered \
    -i 850K_probe.hg19.bed3.gz \
    -r hg19.RefSeq.union.bed.gz \
    -o CpG_density

Useful options include:

-u, --upstream – maximum upstream extension from the TSS in bp (default: 2000)
-d, --downstream – maximum downstream extension from the TES in bp (default: 2000)
-c, --min_gene_size, --SizeCut – minimum transcript span from TSS to TES (default: 200 bp)
--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 density table without generating a plot
-o, --out_prefix, --output – output prefix

Display all options with:

CpG_density_gene_centered -h

For output prefix CpG_density, the command always writes:

The table contains:

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

Use --format both to generate both plot formats.