17. beta_stats.py¶
17.1. Description¶
This program gives basic information on 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
17.2. 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 six 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 The prefix of the output file.
17.3. Input files (examples)¶
17.4. Command¶
$beta_stats.py -r hg19.RefSeq.union.1Kpromoter.bed.gz -i test_02.bed6.gz -o region_stats
17.5. Output files¶
- region_stats.txt