mergeClusters: Manual cluster merging

Description Usage Arguments Details Value Author(s) References Examples

View source: R/mergeClusters.R

Description

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

Usage

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mergeClusters(x, k, table, id, overwrite = FALSE)

Arguments

x

a SingleCellExperiment.

k

character string specifying the clustering to merge; valid values are names(cluster_codes(x)).

table

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.

overwrite

logical specifying whether to force overwriting should a clustering with name id already exist.

Details

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

Value

a SingleCellExperiment with newly added cluster codes stored in cluster_codes(.)$id.

Author(s)

Helena L Crowell helena.crowell@uzh.ch

References

Nowicka M, Krieg C, Crowell HL, 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

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# 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", 
  id = "merging",
  table = merging_table)

# tabulate manual merging
table(cluster_ids(sce, k = "merging"))

# visualize median type-marker expression
plotExprHeatmap(sce, 
  features = "type", 
  by = "cluster_id", 
  k = "merging",
  bars = TRUE)

CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.