rliger (version 1.0.1)

makeInteractTrack: Export predicted gene-pair interaction

Description

Export the predicted gene-pair interactions calculated by upstream function 'linkGenesAndPeaks' into an Interact Track file which is compatible with UCSC Genome Browser.

Usage

makeInteractTrack(corr.mat, genes.list, output_path, path_to_coords)

Value

An Interact Track file stored in the specified path.

Arguments

corr.mat

A sparse matrix with peak names as rows and gene symbols as columns.

genes.list

A list of the genes symbols to be tested. If not specified, this function will use all the gene symbols from the matrix passed to gmat by default.

output_path

Path in which the output file will be stored.

path_to_coords

Path to the gene coordinates file.

Examples

if (FALSE) {
# Only runable for ATAC datasets, see tutorial on GitHub
# some gene-peak correlation matrix: regent
makeInteractTrack(regnet, path_to_coords = 'some_path_to_gene_coordinates/hg19_genes.bed')
}