View source: R/matrix_transformations.R
Transform a .cool file to a sparse upper triangular matrix for input into hic_loess
The plain text file from a .cool file loaded into an R data.frame object. See vignette for more 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.
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.
data('cooler') sparse <- cooler2sparse(cooler) head(sparse)
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