scSEGIndex {scMerge} | R Documentation

## scSEGIndex

### Description

Calculate single-cell Stably Expressed Gene (scSEG) index from Lin. et. al. (2018).

### Usage

    scSEGIndex(exprsMat, cell_type = NULL, ncore = 1)

### Arguments

`exprsMat` | A log-transformed single-cell data, assumed to have no batch effect and covered a wide range of cell types. A n by m matrix, where n is the number of genes and m is the number of cells.
`cell_type` | A vector indicating the cell type information for each cell in the gene expression matrix. If it is `NULL`, the function calculates the scSEG index without using F-statistics.
`ncore` | Number of cores that are used in parallel

### Value

Returns a data frame. Each row is a gene and each column is a statistic relating to the stability of expression of each gene. The main statistic is the `segIdx` column, which is the SEG index.

### Author(s)

Shila Ghazanfar, Yingxin Lin, Pengyi Yang

### References

https://www.biorxiv.org/content/10.1101/229815v2

### Examples

    ## Loading example data
    data('example_sce', package = 'scMerge')
    ## subsetting genes to illustrate usage.
    exprsMat = SummarizedExperiment::assay(example_sce, 'counts')[1:110, 1:20]
    set.seed(1)
    result = scSEGIndex(exprsMat = exprsMat)
    head(result)

[Package scMerge version 1.0.0 Index]