get_de_genes: Find differentially expressed genes

In brickyyyy/MinimizedSC3: Minimized Single-Cell Consensus Clustering

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-values, and thus we advise to use the p-values 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)

brickyyyy/MinimizedSC3 documentation built on May 23, 2019, 1:45 p.m.