GetGeneSets

GetGeneSets takes in a one of the following: "immune.cells","skin.immune.cells","T.subset.cells", or "mouse.cells" and a Seurat Object that will be cell-typed using CAMML. The function will then build a gene.set.collection and a list of gene.weights based on one of the pre-built gene sets.

Creates multi-label cell-types for single-cell RNA-sequencing data based on weighted VAM scoring of cell-type specific gene sets. Schiebout, Frost (2022) <https://psb.stanford.edu/psb-online/proceedings/psb22/schiebout.pdf>.

Courtney Schiebout

CAMML

Cell-Typing using Variance Adjusted Mahalanobis Distances with
Multi-Labeling

H. Robert Frost

GetGeneSets function

<dl><dt>data</dt>
<dd>One of the following: "immune.cells","skin.immune.cells","T.subset.cells", or "mouse.cells".<ul>
<li>"immune.cells" provides gene sets for 5 human immune cells: B, T, NK, Monocytes, and HSCs.</li>
<li>"skin.immune.cells" provides gene sets for 6 human cell types: B, T, NK, Endothelial, Fibroblast, and Monocytes.</li>
<li>"T.subset.cells" provides 6 gene sets for 5 human T cell subtypes: naive CD4, CD4, naive CD8, CD8, memory, and regulatory T cells.</li>
<li>"mouse.cells" provides gene sets for 7 mouse cell types: B, T, NK, DC, Endothelial, Fibroblasts, and Macrophages.</li>
</ul>All datasets were built using differential expression of data in the package celldex using the package EdgeR.</dd>
 
</dl>

Arguments

Get Pre-Built Gene Sets to be applied to CAMML — GetGeneSets

<dl>

<dt>data</dt>
<dd>One of the following: "immune.cells","skin.immune.cells","T.subset.cells", or "mouse.cells".<ul>
<li>"immune.cells" provides gene sets for 5 human immune cells: B, T, NK, Monocytes, and HSCs.</li>
<li>"skin.immune.cells" provides gene sets for 6 human cell types: B, T, NK, Endothelial, Fibroblast, and Monocytes.</li>
<li>"T.subset.cells" provides 6 gene sets for 5 human T cell subtypes: naive CD4, CD4, naive CD8, CD8, memory, and regulatory T cells.</li>
<li>"mouse.cells" provides gene sets for 7 mouse cell types: B, T, NK, DC, Endothelial, Fibroblasts, and Macrophages.</li>
</ul>All datasets were built using differential expression of data in the package celldex using the package EdgeR.</dd>
 
</dl>

GetGeneSets: Get Pre-Built Gene Sets to be applied to CAMML

Description

Usage

Value

Arguments

See Also

Examples