get_de_genes {SC3} | R Documentation

## Find differentially expressed genes

### Description

Differential expression is calculated using the non-parametric Kruskal-Wallis test. A significant `p-value` indicates that gene expression in at least one cluster stochastically dominates one other cluster. Note that the calculation of differential expression after clustering can introduce a bias in the distribution of `p-value`s, and thus we advise to use the `p-value`s for ranking the genes only.

### Usage

    get_de_genes(dataset, labels)

### Arguments

`dataset` | expression matrix
`labels` | cell labels corresponding to the columns of the expression matrix

### Value

a numeric vector containing the differentially expressed genes and correspoding p-values

### Examples

    d <- get_de_genes(yan[1:10,], as.numeric(ann[,1]))
    head(d)

[Package SC3 version 1.10.1 Index]