addClusteringManually: addClusteringManually

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

Description

The function replaces the content of the column "clusters" in the colData(sceObject) with the clustering provided in the user table. The function will return the sceObject with cells which intersect with the cells from the input table.

Usage

addClusteringManually(fileName, sceObject, dataDirectory, experimentName,
  columnName = "clusters")

Arguments

fileName	a file with the clustering solution (for example, from previous CONCLUS runs).
sceObject	a SingleCellExperiment object with your experiment.
dataDirectory	output directory (supposed to be the same for one experiment during the workflow).
experimentName	name of the experiment which appears in filenames (supposed to be the same for one experiment during the workflow).
columnName	name of the column with the clusters.

Value

A SingleCellExperiment object with the created/renewed column "clusters" in the colData(sceObject).

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