6. CpG_distrb_gene_centered

6.1. Overview

CpG_distrb_gene_centered summarizes CpG distribution across prioritized gene-centered genomic annotations.

The genome is partitioned into five annotation classes:

Because transcript annotations can overlap, the classes are made non-overlapping using the following priority:

Higher-priority annotations override lower-priority annotations. For example, a region annotated as both exon and intron is counted as exon.

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 in BED12 format.

Basic usage:

CpG_distrb_gene_centered \
    -i 850K_probe.hg19.bed3.gz \
    -r hg19.RefSeq.union.bed.gz \
    -o geneDist

Useful options include:

-u, --upstream – upstream region size relative to the TSS (default: 2000 bp)
-d, --downstream – downstream region size relative to the TES (default: 2000 bp)
--format {png,pdf,both} – plot output format (default: pdf)
--dpi – PNG resolution (default: 300)
--width – plot width in inches (default: 8)
--height – plot height in inches (default: 6)
--no_plot – write the summary table without generating a plot
-o, --out_prefix, --output – output prefix

Display all options with:

CpG_distrb_gene_centered -h

For output prefix geneDist, the command always writes:

The table contains:

Column	Description
`Priority_order`	Numeric priority of the annotation class.
`Name`	Annotation class.
`Number_of_regions`	Number of non-overlapping intervals in the class.
`Size_of_regions_bp`	Total number of annotated bases.
`CpG_raw_count`	Number of CpGs overlapping the class.
`CpG_count_per_KB`	CpG density per kilobase.

CpG density is calculated as:

\[\mathrm{CpG\ count\ per\ KB} = \frac{\mathrm{CpG\ raw\ count} \times 1000} {\mathrm{Size\ of\ regions\ in\ bp}}\]

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

Use --format both to generate both plot formats.