View source: R/get_cluster_profiles.R
get_cluster_profiles | R Documentation |
Build a consensus copy number profile for each cluster or clone
get_cluster_profiles( cnr, minimum_cells = 3, base.ploidy = 2, cluster.column = "final_cluster" )
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 |
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'.
data(cnr) cnr <- phyloCNR(cnr) cnr <- setBrayClusters(cnr, tree.height = 0.065) cnr <- cluster_heterogeneity(cnr, cluster_column = "BrayC") cnr <- get_cluster_profiles(cnr)
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