renameCellTypes

<code>renameCellTypes</code> Allows you to modify the cell type names for a MOCHA SampleTileObject, from
 the assay names, GRanges column names, and summarizedData (within the metadata), all at once.

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

renameCellTypes function

<dl><dt>MOCHAObject</dt>
<dd>A RangedSummarizedExperiment,</dd>
<dt>oldNames</dt>
<dd>A list of cell type names that you want to change.</dd>
<dt>newNames</dt>
<dd>A list of new cell type names to replace the old names with.</dd></dl>

Arguments

renameCellTypes — renameCellTypes

<dl>

<dt>MOCHAObject</dt>
<dd>A RangedSummarizedExperiment,</dd>


<dt>oldNames</dt>
<dd>A list of cell type names that you want to change.</dd>


<dt>newNames</dt>
<dd>A list of new cell type names to replace the old names with.</dd>

</dl>

renameCellTypes: `renameCellTypes`

Description

Usage

Value

Arguments