14. beta_stats.py¶
14.1. Description¶
This program gives basic information of CpGs located in each genomic region. It adds 6 columns to the input BED file:
Number of CpGs detected in the genomic region
Min methylation level
Max methylation level
Average methylation level across all CpGs
Median methylation level across all CpGs
Standard deviation
14.2. Options¶
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i INPUT_FILE, --input-file-INPUT_FILE
BED6+ file specifying the C position. This BED file should have at least 6 columns (Chrom, ChromStart, ChromeEnd, Name, Beta_value, Strand). Note: the first base in a chromosome is numbered 0. This file can be a regular text file or compressed file (.gz, .bz2)
- -r REGION_FILE, --region-REGION_FILE
BED3+ file of genomic regions. This BED file should have at least 3 columns (Chrom, ChromStart, ChromeEnd).
- -o OUT_FILE, --output-OUT_FILE
Prefix of the output file.
14.3. Input files (examples)¶
14.4. Command¶
$beta_stats.py -r hg19.RefSeq.union.1Kpromoter.bed.gz -i test_02.bed6.gz -o region_stats
14.5. Output files¶
region_stats.txt