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.

- merging codes are accesible through `cluster_codes(x)$id`

- all functions that ask for specification of a clustering (e.g. `plotAbundances`, `plotClusterHeatmap`) take the merging ID as a valid input argument.

### 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]