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:

  1. Number of CpGs detected in the genomic region
  2. Min methylation level
  3. Max methylation level
  4. Average methylation level across all CpGs
  5. Median methylation level across all CpGs
  6. 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)
 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.

17.4. 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