21. beta_stats

21.1. Overview

beta_stats summarizes CpG methylation values within user-defined genomic regions.

For each region, six columns are appended:

CpG_count
Minimum_beta
Maximum_beta
Mean_beta
Median_beta
Standard_deviation

BED coordinates are interpreted as 0-based, half-open intervals.

21.2. Input Files

21.2.1. CpG methylation file

A BED6 or BED6+ file. Column 5 must contain Beta-values. Compressed input is supported.

Example:

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

21.2.2. Region file

A BED3 or BED3+ file containing the genomic regions to summarize. All original region columns are preserved in the output.

Example:

chr1    15864    15865
chr1    18826    18827
chr1    29406    29407

21.3. Usage

Basic usage:

beta_stats \
    -i test_02.bed6.gz \
    -r hg19.RefSeq.union.1Kpromoter.bed.gz \
    -o region_stats

Useful options include:

--header – add a header row to the output
--na_rep – text used when statistics are unavailable (default: NA)
-o, --out_prefix, --output – output prefix

Display all options with:

beta_stats -h

21.4. Output

For output prefix region_stats, the command writes:

region_stats.region_stats.tsv

Invalid region records are retained and filled with the value specified by --na_rep.