makeInteractTrack {rliger} | R Documentation |
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)
[Package rliger version 1.0.1 Index]