get_cluster_profiles: Build a consensus copy number profile for each cluster or...

In SingerLab/gac: Genetic Analysis of Cells

Build a consensus copy number profile for each cluster or clone

Description

Build a consensus copy number profile for each cluster or clone

Usage

get_cluster_profiles(
  cnr,
  minimum_cells = 3,
  base.ploidy = 2,
  cluster.column = "final_cluster"
)

Arguments

cnr	a cnr bundle containing a 'final_cluster' column in Y.
minimum_cells	minimum number of cells in a cluster, best if greater than 3 to estimate a median
base.ploidy	base ploidy of the tumor, default 2 i.e. diploid
cluster.column	column containing clusters

Value

Function returns the cnr with three additional tables. * uclust : number of cells in each final_cluster, only clusters greater than the specified minimum number of cells is shown * DDRC.df: a matrix containing the representative profile for each 'final_cluster' at the bin level. * DDRC.g : interpolation of the DDRC.df at the gene level for each 'final_cluster'.

Examples

data(cnr)

cnr <- phylo_cnr(cnr)

cnr <- setBrayClusters(cnr, tree.height = 0.065)

cnr <- cluster_heterogeneity(cnr, cluster_column = "BrayC")

cnr <- get_cluster_profiles(cnr)

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