calculate_expression

Counts average expression of gene set (Use in package)

Annotating single-cell and spatial-transcriptomic (ST) data based on the Marker dataset. It supports the creation of a unified marker list, Markers_list, using sources including: the package's built-in curated species-specific cell type and marker reference databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI'), Seurat objects containing cell label information, or user-provided Excel tables mapping cell types to markers. Based on the Markers_list, 'SlimR' can calculate gene expression of different cell types and predict annotation information and calculate corresponding AUC by 'Celltype_Calculate()', and annotate it by 'Celltype_Annotation()', then verify it by 'Celltype_Verification()'. At the same time, it can calculate gene expression corresponding to the cell type to generate the corresponding annotation reference map for manual annotation (e.g., 'Heatmap', 'Features plot', 'Combined plot'). For more details see Kabacoff (2020, ISBN:9787115420572).

Zhao qing Wang

SlimR

Marker-Based Package for Single-Cell and Spatial-Transcriptomic
Annotation

calculate_expression function

<dl><dt>object</dt>
<dd>Enter a Seurat object.</dd>
<dt>features</dt>
<dd>Enter one or a set of markers.</dd>
<dt>assay</dt>
<dd>Enter the assay used by the Seurat object, such as "RNA". Default
parameters use "assay = NULL".</dd>
<dt>cluster_col</dt>
<dd>Enter the meta.data column in the Seurat object to be
annotated, such as "seurat_cluster". Default parameters use "cluster_col = NULL".</dd>
<dt>colour_low</dt>
<dd>Color for lowest expression level. (default = "white")</dd>
<dt>colour_high</dt>
<dd>Color for highest expression level. (default = "black")</dd></dl>

Arguments

Counts average expression of gene set (Use in package) — calculate_expression

<dl>

<dt>object</dt>
<dd>Enter a Seurat object.</dd>


<dt>features</dt>
<dd>Enter one or a set of markers.</dd>


<dt>assay</dt>
<dd>Enter the assay used by the Seurat object, such as "RNA". Default
parameters use "assay = NULL".</dd>


<dt>cluster_col</dt>
<dd>Enter the meta.data column in the Seurat object to be
annotated, such as "seurat_cluster". Default parameters use "cluster_col = NULL".</dd>


<dt>colour_low</dt>
<dd>Color for lowest expression level. (default = "white")</dd>


<dt>colour_high</dt>
<dd>Color for highest expression level. (default = "black")</dd>

</dl>

calculate_expression: Counts average expression of gene set (Use in package)

Description

Usage

Value

Arguments

See Also