sc3_calc_biology {SC3} | R Documentation

## Calculate DE genes, marker genes and cell outliers.

### Description

This function calculates differentially expressed (DE) genes, marker genes and cell outliers based on the consensus `SC3` clusterings.

### Usage

    sc3_calc_biology.SingleCellExperiment(object, ks, regime)

    ## S4 method for signature 'SingleCellExperiment'
    sc3_calc_biology(object, ks = NULL,
      regime = NULL)

### Arguments

`object` | an object of `SingleCellExperiment` class
`ks` | a continuous range of integers - the number of clusters `k` to be used for SC3 clustering. Can also be a single integer.
`regime` | defines what biological analysis to perform. "marker" for marker genes, "de" for differentiall expressed genes and "outl" for outlier cells

### Details

DE genes are calculated using `get_de_genes`. Results of the DE analysis are saved as new columns in the `featureData` slot of the input `object`. The column names correspond to the adjusted `p-value`s of the genes and have the following format: `sc3_k_de_padj`, where `k` is the number of clusters.

Marker genes are calculated using `get_marker_genes`. Results of the marker gene analysis are saved as three new columns (for each `k`) to the `featureData` slot of the input `object`. The column names correspond to the `SC3` cluster labels, to the adjusted `p-value`s of the genes and to the area under the ROC curve and have the following format: `sc3_k_markers_clusts`, `sc3_k_markers_padj` and `sc3_k_markers_auroc`, where `k` is the number of clusters.

Outlier cells are calculated using `get_outl_cells`. Results of the cell outlier analysis are saved as new columns in the `phenoData` slot of the input `object`. The column names correspond to the `log2(outlier_score)` and have the following format: `sc3_k_log2_outlier_score`, where `k` is the number of clusters.

Additionally, `biology` item is added to the `sc3` slot and is set to `TRUE` indicating that the biological analysis of the dataset has been performed.

### Value

an object of `SingleCellExperiment` class

[Package SC3 version 1.16.0 Index]