getMarkerGenes: Get top N marker genes from each cluster.

In PolinaPavlovich/CONCLUS: ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

Description

This function reads results of conclus::rankGenes() from "dataDirectory/marker_genes" and selects top N markers for each cluster.

Usage

getMarkerGenes(dataDirectory, sceObject, genesNumber = 14,
  experimentName, removeDuplicates = TRUE)

Arguments

dataDirectory	output directory for a run of CONCLUS (supposed to be the same for one experiment during the workflow).
sceObject	a SingleCellExperiment object with your experiment.
genesNumber	top N number of genes to get from one cluster.
experimentName	name of the experiment which appears in filenames (supposed to be the same for one experiment during the workflow).
removeDuplicates	boolean, if duplicated genes must be deleted or not.

Value

A data frame where the first columns are marker genes ("geneName") and the second column is the groups ("clusters").

PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.