example_data_compare

A list containing example single-cell multi-omics data used in "compare" mode of the <code>scPOEM</code> package.

datasets

Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via 'Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in 'scTenifoldNet'. See <doi:10.1093/bioinformatics/btaf483> for more details.

Yuntong Hou

scPOEM

Single-Cell Meta-Path Based Omic Embedding

Yan Zhong

Yeran Chen

Youshi Chang

Yongjian Yang

Xinyue Zheng

James Cai

example_data_compare function

A named list of length 2. Each element is itself a named list with the following components:<dl>
<dt><code>X</code></dt>
<dd>The scATAC-seq data, sparse matrix.</dd><dt><code>Y</code></dt>
<dd>The scRNA-seq data, sparse matrix.</dd><dt><code>peak_data</code></dt>
<dd>A data.frame containing peak information.</dd><dt><code>gene_data</code></dt>
<dd>A data.frame containing gene information (must contain column "gene_name").</dd><dt><code>cell_data</code></dt>
<dd>A data.frame containing cell metadata.</dd><dt><code>neibor_peak</code></dt>
<dd>The peak IDs within a certain range of each gene, must have cols c("gene_name", "start_use", "end_use"). The id numbers in "start_use" and "end_use" are start from 0.</dd><dt><code>genome</code></dt>
<dd>The genome length for the species.</dd>
</dl>

Format

Example Input Data for Compare Mode Analysis — example_data_compare

A named list of length 2. Each element is itself a named list with the following components:<dl>
<dt><code>X</code></dt>
<dd>The scATAC-seq data, sparse matrix.</dd>

<dt><code>Y</code></dt>
<dd>The scRNA-seq data, sparse matrix.</dd>

<dt><code>peak_data</code></dt>
<dd>A data.frame containing peak information.</dd>

<dt><code>gene_data</code></dt>
<dd>A data.frame containing gene information (must contain column "gene_name").</dd>

<dt><code>cell_data</code></dt>
<dd>A data.frame containing cell metadata.</dd>

<dt><code>neibor_peak</code></dt>
<dd>The peak IDs within a certain range of each gene, must have cols c("gene_name", "start_use", "end_use"). The id numbers in "start_use" and "end_use" are start from 0.</dd>

<dt><code>genome</code></dt>
<dd>The genome length for the species.</dd>


</dl>

example_data_compare: Example Input Data for Compare Mode Analysis

Description

Usage

Arguments

Format

Examples