scSEGIndex {scMerge} | R Documentation |
Calculate single-cell Stably Expressed Gene (scSEG) index from Lin. et. al. (2018).
scSEGIndex(exprsMat, cell_type = NULL, ncore = 1)
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 |
ncore |
Number of cores that are used in parallel |
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.
Shila Ghazanfar, Yingxin Lin, Pengyi Yang
https://www.biorxiv.org/content/10.1101/229815v2
## 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)