Run Phenograph based clustering.
Arguments
- fcd
flow cytometry dataset.
- input_type
data to use for the calculation, e.g. "expr" or "pca" (suggested: "pca").
- data_slot
data slot to use for the calculation, e.g. "orig" or "norm".
- k
K value used for clustering.
- seed
A seed is set for reproducibility.
- prefix
Optional prefix for the slot name of the output.
- nPC
Number of principal components to use for the analysis.
- markers
vector of marker names to include or exclude from the calculation according to the discard parameter. See functions used_markers and measured_markers for the extraction of markers directly from the condor object
- discard
LOGICAL if the markers specified should be included, "F", or excluded, "T", from the calculation. Default = F.