getCoverage

getCoverage takes the output of MOCHA::getPopFrags and returns
 a GRanges of singe-basepair resolution coverage.

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

getCoverage function

<dl><dt>popFrags</dt>
<dd>GRangesList of fragments for all sample/cell populations</dd>
<dt>normFactor</dt>
<dd>Normalization factor. Can be either be one, in which case all coverage files will be normalized by the same value, or the same length as the GRangesList</dd>
<dt>TxDb</dt>
<dd>The TxDb-class transcript annotation
package for your organism (e.g. "TxDb.Hsapiens.UCSC.hg38.refGene"). This
must be installed. See
<a href="https://bioconductor.org/packages/release/data/annotation/">
Bioconductor AnnotationData Packages</a>.</dd>
<dt>cl</dt>
<dd>cl argument to <code>pblapply</code></dd>
<dt>filterEmpty</dt>
<dd>True/False flag on whether or not to carry forward regions without coverage.</dd>
<dt>verbose</dt>
<dd>Boolean variable to determine verbosity of output.</dd></dl>

Arguments

Get sample-specific coverage files for each sample-cell population. — getCoverage

<dl>

<dt>popFrags</dt>
<dd>GRangesList of fragments for all sample/cell populations</dd>


<dt>normFactor</dt>
<dd>Normalization factor. Can be either be one, in which case all coverage files will be normalized by the same value, or the same length as the GRangesList</dd>


<dt>TxDb</dt>
<dd>The TxDb-class transcript annotation
package for your organism (e.g. "TxDb.Hsapiens.UCSC.hg38.refGene"). This
must be installed. See
<a href='https://bioconductor.org/packages/release/data/annotation/'>
Bioconductor AnnotationData Packages</a>.</dd>


<dt>cl</dt>
<dd>cl argument to <code>pblapply</code></dd>


<dt>filterEmpty</dt>
<dd>True/False flag on whether or not to carry forward regions without coverage.</dd>


<dt>verbose</dt>
<dd>Boolean variable to determine verbosity of output.</dd>

</dl>

getCoverage: Get sample-specific coverage files for each sample-cell population.

Description

Usage

Value

Arguments