LM22

Newman et al.'s 2015 22 leukocyte signature matrix.

datasets

Tools to construct (or add to) cell-type signature matrices using flow sorted or single cell samples and deconvolve bulk gene expression data.
Useful for assessing the quality of single cell RNAseq experiments, estimating the accuracy of signature matrices, and determining cell-type spillover.
Please cite: Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells <doi:10.1371/journal.pone.0224693>.

Samuel Danziger

ADAPTS

Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells

LM22 function

A data frame with 547 observations on the following 22 variables.<dl>
 <dt><code>B.cells.naive</code></dt>
<dd>a numeric vector</dd> <dt><code>B.cells.memory</code></dt>
<dd>a numeric vector</dd> <dt><code>Plasma.cells</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.CD8</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.CD4.naive</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.CD4.memory.resting</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.CD4.memory.activated</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.follicular.helper</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.regulatory..Tregs.</code></dt>
<dd>a numeric vector</dd> <dt><code>T.cells.gamma.delta</code></dt>
<dd>a numeric vector</dd> <dt><code>NK.cells.resting</code></dt>
<dd>a numeric vector</dd> <dt><code>NK.cells.activated</code></dt>
<dd>a numeric vector</dd> <dt><code>Monocytes</code></dt>
<dd>a numeric vector</dd> <dt><code>Macrophages.M0</code></dt>
<dd>a numeric vector</dd> <dt><code>Macrophages.M1</code></dt>
<dd>a numeric vector</dd> <dt><code>Macrophages.M2</code></dt>
<dd>a numeric vector</dd> <dt><code>Dendritic.cells.resting</code></dt>
<dd>a numeric vector</dd> <dt><code>Dendritic.cells.activated</code></dt>
<dd>a numeric vector</dd> <dt><code>Mast.cells.resting</code></dt>
<dd>a numeric vector</dd> <dt><code>Mast.cells.activated</code></dt>
<dd>a numeric vector</dd> <dt><code>Eosinophils</code></dt>
<dd>a numeric vector</dd> <dt><code>Neutrophils</code></dt>
<dd>a numeric vector</dd> 
</dl>

Format

Leukocyte 22 data matrix — LM22

A data frame with 547 observations on the following 22 variables.<dl>
 <dt><code>B.cells.naive</code></dt>
<dd>a numeric vector</dd>

 <dt><code>B.cells.memory</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Plasma.cells</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.CD8</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.CD4.naive</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.CD4.memory.resting</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.CD4.memory.activated</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.follicular.helper</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.regulatory..Tregs.</code></dt>
<dd>a numeric vector</dd>

 <dt><code>T.cells.gamma.delta</code></dt>
<dd>a numeric vector</dd>

 <dt><code>NK.cells.resting</code></dt>
<dd>a numeric vector</dd>

 <dt><code>NK.cells.activated</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Monocytes</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Macrophages.M0</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Macrophages.M1</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Macrophages.M2</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Dendritic.cells.resting</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Dendritic.cells.activated</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Mast.cells.resting</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Mast.cells.activated</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Eosinophils</code></dt>
<dd>a numeric vector</dd>

 <dt><code>Neutrophils</code></dt>
<dd>a numeric vector</dd>

 
</dl>

LM22: Leukocyte 22 data matrix

Description

Usage

Arguments

Format

Examples