binaryDDRC: binaryDDRC

View source: R/binary.cnr.R

binaryDDRCR Documentation

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 <- phyloCNR(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 Oct. 14, 2022, 4:09 a.m.