Genotype: Genotype each cell for each region and plot the genotypes.

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

Genotype each cell for each region and plot the genotypes.

Description

Genotype each cell for each region and plot the genotypes.

Usage

Genotype(
  Obj_filtered = NULL,
  xmax = NULL,
  plot_path = NULL,
  rds_path = NULL,
  ref_gt = NULL,
  cell_type = NULL,
  maxcp = 6,
  legend = FALSE
)

Arguments

Obj_filtered	An Alleloscope object with a n cell by (m region * 4) genotype_values matrix. Every 2 columns in the genotype_table matrix are (rho_hat, theta_hat) of each region.
xmax	An integer for the x-axis maximum limit.
plot_path	The path for saving the plot.
rds_path	The path for saving the rds object.
ref_gt	A reference "genotypes" (from scDNA-seq) to help with genotype estimation.
cell_type	A matrix with two columns: COL1- cell barcodes; COL2- cell types ("tumor" and others)
maxcp	Integer. Setting the maximum number of copies for the analysis.
legend	Logical (TRUE/FALSE) Whether or not to show the figure legends.

Value

A list of ggplot objects of the genotyping results for all the regions.

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