Brick_mcool_normalisation_exists: Check if a normalisation exists in an mcool file.

In koustav-pal/HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

Check if a normalisation exists in an mcool file.

Description

Brick_mcool_normalisation_exists checks if a particular normalisation exists in an mcool file.

Usage

Brick_mcool_normalisation_exists(mcool, norm_factor = NULL, resolution = NULL)

Arguments

mcool	Required. Path to an mcool file.
norm_factor	Required. The normalization factor to use for normalization from an mcool file. norm_factor currently accepts one of "Iterative-Correction", "Knight-Ruitz", "Vanilla-coverage", "Vanilla-coverage-square-root".
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Value

A boolean vector of length 1

Examples

## Not run: 

require(curl)
out_dir <- file.path(tempdir(), "mcool_test_dir")
dir.create(path = out_dir)
curl_download(url = paste("https://data.4dnucleome.org/",
"files-processed/4DNFI7JNCNFB/",
"@download/4DNFI7JNCNFB.mcool", sep = ""),
destfile = file.path(out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool"))

mcool <- file.path(out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
Brick_mcool_normalisation_exists(mcool = mcool,
norm_factor = "Iterative-Correction",
resolution = 50000)


## End(Not run)

koustav-pal/HiCBricks documentation built on Oct. 25, 2022, 12:06 a.m.