rliger: makeInteractTrack – R documentation

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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)

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: 
# some gene-peak correlation matrix: regent 
makeInteractTrack(regnet, path_to_coords = 'some_path_to_gene_coordinates/hg19_genes.bed')

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18