AssignClones_ref: Using marker regions to assign each cell into c reference...

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

Using marker regions to assign each cell into c reference subclones

Description

The genotypes (rho, theta) are: 1.(0.5,0); 2.(0.5,1); 3.(1,0); 4.(1,0.5); 5.(1,1); 6.(1.5,0); 7.(1.5,1/3); 8.(1.5,2/3); 9.(1.5,1); 10.(2,0); 11.(2,1/4); 12.(2,2/4); 13.(2,3/4); 14.(2,4/4) 15.(2.5,0); 16.(2.5,1/5); 17.(2.5,2/5); 18.(2.5,3/5); 19.(2.5,4/5); 20.(2.5,1); 21.(3,0); 22.(3,1/6); 23.(3,2/6); 24.(3,3/6); 25.(3,4/6); 26.(3,5/6); 27.(3,6/6)

Usage

AssignClones_ref(
  Obj_filtered = NULL,
  priorCloneProbs = NULL,
  clone.genotypes,
  sigma.rho = 0.25
)

Arguments

Obj_filtered	An Alleloscope object with a n cell by (m region * 4) genotype_values matrix. Every 4 columns in the genotype_table matrix are (rho_hat, theta_hat, h1, h2) of each region. h1, h2 are the coverage across all SNPs located on the major haplotype (h1) and the minor haplotype (h2) in a region for each cell.
priorCloneProbs:	A numeric vector indicating prior prior probability of each subclone.
clone.genotypes:	c by m matrix of numbers representing different genotypes for each clone and each maker region (known from scDNA-seq).
sigma.rho:	Numeric. Standard deviation of the rho_i values under normal distribution.

seasoncloud/Alleloscope documentation built on March 17, 2023, 1:14 a.m.