This data contains expression levels (log-transformed and centered) for 50 cells and 2000 genes.
 The 50 cells are randomly assigned to two cell types and three cell-cycle stages.
 400 genes are assigned as cell-cycle genes, and the other 1600 genes are control genes.
 For descriptions of how we generated this data, please refer to the paper.

datasets

Implements a method for identifying and removing
the cell-cycle effect from scRNA-Seq data. The description of the
method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing
the cell-cycle effect from single-cell RNA-Sequencing data. Submitted.
Different from previous methods, ccRemover implements a mechanism that
formally tests whether a component is cell-cycle related or not, and thus
while it often thoroughly removes the cell-cycle effect, it preserves
other features/signals of interest in the data.

Jun Li

ccRemover

Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing
Data

Martin Barron

dat function

A list that contains the following attributes (only <code>x</code> and <code>if.cc</code> are used by ccRemover.main.)<dl class="dl-horizontal">
		<dt><code>x</code></dt><dd>the data matrix. rows are genes, and columns are cells. These should be treated as log-transformed and
		centered (each row has mean 0) expression levels.</dd>
		<dt><code>if.cc</code></dt><dd>a vector of values FALSE's or TRUE's, denoting whether the genes are cell-cycle related or control.</dd>
		<dt><code>n</code></dt><dd>the number of cells. n=ncol(x).</dd>
		<dt><code>p</code></dt><dd>the number of genes. p=nrow(x).</dd>
		<dt><code>pc</code></dt><dd>the number of cell-cycle genes. pc=sum(if.cc).</dd>
		<dt><code>ct</code></dt><dd>cell types. a vector of values 1 and 2.</dd>
		<dt><code>cc</code></dt><dd>cell-cycle stages. a vector of values 1, 2, or 3.</dd>
 </dl>

Format

A simulated scRNA-Seq data. — dat

A list that contains the following attributes (only <code>x</code> and <code>if.cc</code> are used by ccRemover.main.)<dl class='dl-horizontal'>
		<dt><code>x</code></dt><dd>the data matrix. rows are genes, and columns are cells. These should be treated as log-transformed and
		centered (each row has mean 0) expression levels.</dd>
		<dt><code>if.cc</code></dt><dd>a vector of values FALSE's or TRUE's, denoting whether the genes are cell-cycle related or control.</dd>
		<dt><code>n</code></dt><dd>the number of cells. n=ncol(x).</dd>
		<dt><code>p</code></dt><dd>the number of genes. p=nrow(x).</dd>
		<dt><code>pc</code></dt><dd>the number of cell-cycle genes. pc=sum(if.cc).</dd>
		<dt><code>ct</code></dt><dd>cell types. a vector of values 1 and 2.</dd>
		<dt><code>cc</code></dt><dd>cell-cycle stages. a vector of values 1, 2, or 3.</dd>
 </dl>

dat: A simulated scRNA-Seq data.

Description

Usage

Arguments

Value

Format