get_de_genes: Find differentially expressed genes

Description Usage Arguments Value Examples

View source: R/ShinyFunctions.R

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

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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

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

SC3 documentation built on Nov. 1, 2018, 4:24 a.m.