mergeClusters {CATALYST}R Documentation

Manual cluster merging

Description

mergeClusters provides a simple wrapper to store a manual merging inside the input SingleCellExperiment.

Usage

mergeClusters(x, k, table, id)

Arguments

x

a SingleCellExperiment.

k

a character string specifying the clustering to merge. Should be one of colnames(cluster_codes(x)).

table

a merging table with 2 columns containing the cluster IDs to merge in the 1st, and the cluster IDs to newly assign in the 2nd column.

id

character string. Used as a label for the merging.

Details

in the following code snippets, x is a SingleCellExperiment object.

Value

Writes the newly assigend cluster codes into the metadata slot cluster_codes of the input SingleCellExperiment and returns the latter.

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

References

Nowicka M, Krieg C, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

Examples

# construct SCE & run clustering
data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce)

# merge clusters
sce <- mergeClusters(sce, k="meta20", table=merging_table, id="merging")
plotClusterHeatmap(sce, k="merging", hm2="pS6")


[Package CATALYST version 1.10.3 Index]