makeInteractTrack-deprecated

Export the predicted gene-pair interactions calculated by
upstream function <code>linkGenesAndPeaks</code> into an Interact Track file
which is compatible with <a href="https://genome.ucsc.edu/cgi-bin/hgCustom">UCSC
Genome Browser</a>.

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

Andrew Robbins

makeInteractTrack-deprecated function

<dl><dt>corr.mat</dt>
<dd>A sparse matrix of correlation with peak names as rows and
gene names as columns.</dd>
<dt>path_to_coords</dt>
<dd>Path to the gene coordinates file.</dd>
<dt>genes.list</dt>
<dd>Character vector of gene names to be exported. Default
<code>NULL</code> uses all genes available in <code>corrMat</code>.</dd>
<dt>output_path</dt>
<dd>Path of filename where the output file will be stored. If
a folder, a file named <code>"Interact_Track.bed"</code> will be created. Default
current working directory.</dd></dl>

Arguments

Export the predicted gene-pair interactions calculated by
upstream function <code>linkGenesAndPeaks</code> into an Interact Track file
which is compatible with <a href='https://genome.ucsc.edu/cgi-bin/hgCustom'>UCSC
Genome Browser</a>.

[Deprecated] Export predicted gene-pair interaction — makeInteractTrack-deprecated

<dl>

<dt>corr.mat</dt>
<dd>A sparse matrix of correlation with peak names as rows and
gene names as columns.</dd>


<dt>path_to_coords</dt>
<dd>Path to the gene coordinates file.</dd>


<dt>genes.list</dt>
<dd>Character vector of gene names to be exported. Default
<code>NULL</code> uses all genes available in <code>corrMat</code>.</dd>


<dt>output_path</dt>
<dd>Path of filename where the output file will be stored. If
a folder, a file named <code>"Interact_Track.bed"</code> will be created. Default
current working directory.</dd>

</dl>

makeInteractTrack-deprecated: [Deprecated] Export predicted gene-pair interaction

Description

Value

Arguments

See Also