binaryDDRC: binaryDDRC

In SingerLab/gac: Genetic Analysis of Cells

binaryDDRC

Description

binaryDDRC

Usage

binaryDDRC(ddrc, base.ploidy = 2)

Arguments

ddrc	a DDRC.df or DDRC.g matrix belonging to a cnr object
base.ploidy	expected cell ploidy, e.g. 2N = 2, 4N = 4.

Value

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.

Examples

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)

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.