setBrayClusters | R Documentation |
Set Bray clusters
setBrayClusters(
cnr,
tree.height = NULL,
prefix = "C",
opt.method = "maxp",
...
)
cnr |
a cnr bundle |
tree.height |
height of the tree |
prefix |
a prefix to append before the cluster number |
opt.method |
optimization method, must be either "mi" or 'maxp' ; default is 'mi' |
... |
additional parameters passed to optClust |
Returns a cnr object with cluster membership based on Bray-Curtis
Ward.D2 heirarchical clustering. If method is "mi"
the
the tree height is calculated using minimum.intersect
.
Where optimal height is the value at the intersect between the number of
one-cell and multi-cell clusters. If method is "maxp"
,
data(cnr)
noisy.cells <- cnr$qc$cellID[cnr$qc$qc.status == "FAIL"]
cnr <- excludeCells(cnr, excl = noisy.cells)
cnr <- phylo_cnr(cnr, root.cell = "cell0")
cnr <- setBrayClusters(cnr)
cnr <- setBrayClusters(cnr, opt.method = "maxp")
cnr <- setBrayClusters(cnr, tree.height = 0.16)
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