FindMarkers: Find DE genes

In debsin/dropClust: Single Cell Transcriptome Analysis

Description

Find cluster specific differentially expressed genes

Usage

FindMarkers(object, selected_clusters = NA, lfc_th, q_th, nDE = 30)

Arguments

object	A SingleCellExperiment object containing normalized expression values in "normcounts".
selected_clusters	vector of selected cluster identifier to be considered. When unspecified (=NA), defaults to all predicted clusters.
lfc_th	numeric, [0,1] log2 fold change threshold value to define significance.
q_th	numeric, [0,1] fdr adjusted p-value to define significance.
nDE	integer, specifies the number of DE genes to return per cluster default = 30.

Details

Performs significance tests in one-vs-all manner to determine cluster specific genes: two-sample Wilcoxon ('Mann-Whitney') test followed by 'fdr' adjustment and log-fold-change.

Value

list containing:

• DE_up vector of unique DE gene names
  

• DE_res list of data frames for respective cluster specific DE genes, each row of a data frame mentions the gene significant pvalues, qvalues and LFC values

debsin/dropClust documentation built on Nov. 4, 2019, 10:22 a.m.