differentialsToGRanges

<code>differentialsToGRanges</code> Converts a data.frame matrix to a GRanges,
 preserving additional columns as GRanges metadata

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

differentialsToGRanges function

<dl><dt>differentials</dt>
<dd>a matrix/data.frame with a column tileColumn containing
region strings in the format "chr:start-end"</dd>
<dt>tileColumn</dt>
<dd>name of column containing region strings. Default is "Tile".</dd></dl>

Arguments

differentialsToGRanges Converts a data.frame matrix to a GRanges,
  preserving additional columns as GRanges metadata — differentialsToGRanges

<dl>

<dt>differentials</dt>
<dd>a matrix/data.frame with a column tileColumn containing
region strings in the format "chr:start-end"</dd>


<dt>tileColumn</dt>
<dd>name of column containing region strings. Default is "Tile".</dd>

</dl>

differentialsToGRanges: `differentialsToGRanges` Converts a data.frame matrix to a GRanges, preserving additional columns as GRanges metadata

Description

Usage

Value

Arguments