readCoolNorms: Read normalizations included in .(m)cool files

In PhanstielLab/plotgardener: Coordinate-Based Genomic Visualization Package for R

Read normalizations included in .(m)cool files

Description

Read normalizations included in .(m)cool files

Usage

readCoolNorms(file, resolution = NULL)

Arguments

file	A character value specifying the path to the .(m)cool file
resolution	optional, specify which resolution(s) to read normalization types from. Default is all resolutions in 'file'.

Details

The "BALANCE" normalization refers to applying the pre-calculated matrix balancing weights in the 'weight' dataset of 'file', typically present in files created using cooler. VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR is Knight-Ruiz normalization.

Please note that if using a file from HiC-Pro, ICE normalizations will come from files stored in a separate folder, and thus will not contain any normalizations explicitly called "ICE" or "BALANCE" since values are included already normalized. This normalization can be specified as "NONE".

Value

A vector or list of vectors of available normalizations

Author(s)

Sarah Parker, Nicole Kramer

PhanstielLab/plotgardener documentation built on Feb. 27, 2025, 8:22 p.m.