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.

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 1.6.7 Index]