rankGenes: Rank marker genes by statistical significance.

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

Description

This function searches marker genes for each cluster. It saves tables in the "dataDirectory/marker_genes" directory, one table per cluster.

Usage

rankGenes(sceObject, clustersSimilarityMatrix, dataDirectory,
  experimentName, column = "clusters")

Arguments

sceObject	a SingleCellExperiment object with your experiment.
clustersSimilarityMatrix	matrix, result of conclus::calculateClustersSimilarity() function.
dataDirectory	output directory for CONCLUS (supposed to be the same for one experiment during the workflow).
experimentName	name of the experiment which will appear in filenames (supposed to be the same for one experiment during the workflow).
column	name of the column with a clustering result.

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