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, table, id)

## S4 method for signature 'daFrame'
mergeClusters(x, table, id)

Arguments

x

a daFrame.

table

the merging table; a data.frame with columns 'old_cluster', 'new_cluster' and 'label'.

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 crowellh@student.ethz.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
lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33", 
    "CD123", "CD14", "IgM", "HLA_DR", "CD7")
re <- cluster(re, cols_to_use=lineage)

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

[Package CATALYST version 1.4.2 Index]