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

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

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 Feb. 21, 2022, 9:57 a.m.