4.1.6. statshic.py

Compute basic statistics about the given Hi-C dataset.

The statistics are the following:

  • Mean
  • Standard deviation
  • Median
  • Percentiles at 10, 25, 75 and 95%

Also report the dimensions of the matrices and their size (number of elements). For the whole datasets, only the size is given.

created:August 2018
last modified:August 2018

4.1.6.1. Usage

Compute basic statistics about the given Hi-C dataset. The results are printed to standard output or written as JSON.

usage: statshic [-h] [-w] [-o OUTPUT] hic

4.1.6.1.1. Positional Arguments

hic the Hi-C directory with the metadata.json file

4.1.6.1.2. Named Arguments

-w, --whole-dataset
 

compute also the stats on the whole dataset; may use a lot of memory

Default: False

-o, --output the output file, in JSON