mergeClusters {CATALYST} | R Documentation

## Manual cluster merging

### Description

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

### Usage

    mergeClusters(x, k, table, id)

    ## S4 method for signature 'daFrame,character,data.frame,character'
    mergeClusters(x, k,
      table, id)

### Arguments

`x` | a `daFrame`.
`k` | a character string specifying the clustering to merge.
`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.
`...` | optional arguments.

### Details

in the following code snippets, `x` is a `daFrame` 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 `daFrame` 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

    data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
    re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

    # run clustering
    re <- cluster(re)

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

[Package CATALYST version 1.8.7 Index]