makeInteractTrack: Export predicted gene-pair interaction

In rliger: Linked Inference of Genomic Experimental Relationships

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)

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.

Value

An Interact Track file stored in the specified path.

Examples

## Not run: 
# 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')

## End(Not run)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.