15. beta_profile_region.py

15.1. Description

This program calculates methylation profile (i.e. average beta value) around the user-specified genomic regions.

Example of input

# BED6 format (INPUT_FILE)
chr22   44021512        44021513        cg24055475      0.9231  -
chr13   111568382       111568383       cg06540715      0.1071  +
chr20   44033594        44033595        cg21482942      0.6122  -

# BED3 format (REGION_FILE)
chr1    15864   15865
chr1    18826   18827
chr1    29406   29407

15.2. 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). BED6+ 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 three columns (Chrom, ChromStart, ChromeEnd). If the 6-th column does not exist, all regions will be considered as on “+” strand.

-d DOWNSTREAM_SIZE, --downstream=DOWNSTREAM_SIZE

Size of extension to downstream. default=2000 (bp)

-u UPSTREAM_SIZE, --upstream=UPSTREAM_SIZE

Size of extension to upstream. default=2000 (bp)

-o OUT_FILE, --output=OUT_FILE

The prefix of the output file.

15.3. Input files (examples)

15.4. Command

$beta_profile_region.py -r hg19.RefSeq.union.1Kpromoter.bed.gz -i test_02.bed6.gz -o region_profile

15.5. Output files

region_profile.txt
region_profile.r
region_profile.pdf