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]