baseline.GMM: pre-define a group of normal cells with GMM.

In navinlabcode/copykat: COPYKAT: Inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNA-seq data

pre-define a group of normal cells with GMM.

Description

pre-define a group of normal cells with GMM.

Usage

baseline.GMM(
  CNA.mat,
  max.normal = 5,
  mu.cut = 0.05,
  Nfraq.cut = 0.99,
  RE.before = basa,
  n.cores = 1
)

Arguments

CNA.mat	smoothed data matrix; genes in rows; cell names in columns.
max.normal	find the first number diploid cells to save efforts.
mu.cut	diploid baseline cutoff.
Nfraq.cut	minimal fractoins of genomes with CNAs.

Value

1) predefined diploid cell names; 2) clustering results; 3) inferred baseline.

Examples

test.gmm <- baseline.GMM(CNA.mat=smooth.com, max.normal=30, mu.cut=0.05, Nfraq.cut=0.99)

test.gmm.cells <- test.bnc$preN

navinlabcode/copykat documentation built on June 29, 2024, 2:31 a.m.