cooler2sparse {HiCcompare} | R Documentation

## Transform a .cool file to a sparse upper triangular matrix for input into hic_loess

### Description

Transform a .cool file to a sparse upper triangular matrix for input into hic_loess

### Usage

    cooler2sparse(cooler)

### Arguments

`cooler` | The plain text file from a .cool file loaded into an R data.frame object. See vignette for more details.

### Details

The .cool format is linked a database of Hi-C experiments and allows access to many sets of Hi-C data which can be found at the Index of Coolers ftp://cooler.csail.mit.edu/coolers. Once a .cool file is dumped into a contact matrix in plain text it can be read into R. This function provides a method for converting the .cool matrix into a sparse upper triangular matrix ready to be entered into hic_loess.

### Value

A Sparse upper triangular matrix or a list of sparse upper triangular matrices. If the .cool file contains data for more than one chromosome The function will split the data up into a list of matrices, one per chromosome.

### Examples

    data('cooler')
    sparse <- cooler2sparse(cooler)
    head(sparse)

[Package HiCcompare version 1.9.0 Index]