singlePopulationSampleTileMatrix

<code>singlePopulationSampleTileMatrix</code> is a function that can transform
 a set of tile intensities into peak X sample matrix for a custom set of tiles

internal

A statistical framework and analysis tool for open chromatin
analysis designed specifically for single cell ATAC-seq (Assay for
Transposase-Accessible Chromatin) data, after cell type/cluster
identification. These novel modules remove unwanted technical variation,
identify open chromatin, robustly models repeated measures in single cell
data, implement advanced statistical frameworks to model zero-inflation for
differential and co-accessibility analyses, and integrate with existing
databases and modules for downstream analyses to reveal biological insights.
MOCHA provides a statistical foundation for complex downstream analysis to
help advance the potential of single cell ATAC-seq for applied studies.
Methods for zero-inflated statistics are as described in:
Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>.
Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated
Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Imran McGrath

MOCHA

Modeling for Single-Cell Open Chromatin Analysis

Samir Rachid Zaim

Mark-Phillip Pebworth

Lauren Okada

Xiaojun Li

singlePopulationSampleTileMatrix function

<dl><dt>peaksExperiment</dt>
<dd>peakset RaggedExperiment, one celltype from the output of callOpenTiles</dd>
<dt>consensusTiles</dt>
<dd>a vector containing the tileIDs to subset the
sample-tile matrix</dd></dl>

Arguments

singlePopulationSampleTileMatrix — singlePopulationSampleTileMatrix

<dl>

<dt>peaksExperiment</dt>
<dd>peakset RaggedExperiment, one celltype from the output of callOpenTiles</dd>


<dt>consensusTiles</dt>
<dd>a vector containing the tileIDs to subset the
sample-tile matrix</dd>

</dl>

singlePopulationSampleTileMatrix: `singlePopulationSampleTileMatrix`

Description

Usage

Value

Arguments

Details

References