binaryDDRC | R Documentation |
binaryDDRC
binaryDDRC(ddrc, base.ploidy = 2)
ddrc |
a DDRC.df or DDRC.g matrix belonging to a cnr object |
base.ploidy |
expected cell ploidy, e.g. 2N = 2, 4N = 4. |
returns a binary/incidence matrix for a DDRC object. A value of 1 is returned for all values not equal to the cell ploidy. Currently being used to create an infScite table using clones.
data(cnr)
noisy.cells <- cnr$qc$cellID[cnr$qc$qc.status == "FAIL"]
## reduced pipeline to genrate DDRC clone profiles
cnr <- excludeCells(cnr, excl = noisy.cells)
cnr <- phylo_cnr(cnr, root.cell = "cell0")
cnr <- setBrayClusters(cnr)
cnr <- run_consensus_clustering(cnr, iters = 20, maxK = 40)
cnr <- doKSpectral(cnr)
cnr <- setKcc(cnr)
cnr <- cluster_heterogeneity(cnr, by = "category1",
cluster_column = "ConsensusC")
cnr <- get_cluster_profiles(cnr)
binary.ddrc <- binaryDDRC(cnr$DDRC.df)
head(binary.ddrc)
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