Est_regions: Perform EM iterations on the filtered cells with barcodes,...

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

Perform EM iterations on the filtered cells with barcodes, and plot the results for each region.

Description

Perform EM iterations on the filtered cells with barcodes, and plot the results for each region.

Usage

Est_regions(
  Obj_filtered = NULL,
  max_nSNP = 30000,
  plot_stat = TRUE,
  min_cell = 5,
  min_snp = 0,
  rds_path = NULL,
  cont = FALSE,
  max_iter = 50,
  phases = NULL,
  sub_cells = NULL,
  sub_region = NULL
)

Arguments

Obj_filtered	An Alleloscope object with allele and segment information for estimating cell major haplotype proportion (theta_hat) for each region.
max_nSNP	Integer. Maximum SNP number used for estimating theta_hat for a region.
plot_stat	Logical (TRUE/ FALSE). Whether or not to plot the statistics and EM results for each region.
min_cell	Integer. Filter out the cells with reads < min_cells.
min_snp	Integer. Filter out the SNPs with reads < min_snp.
rds_path	The path for saving the rds files for the estimated results for each region.
cont	Logical (TRUE/FALSE). Whether or not to skip the regions with the rds files in the specified rds_path.
max_iter	Integer. Maximum numbers of EM iterations.
phases	List. The estimated phase indicators (I_j) of each SNP across all regions.
sub_cells	A vector of cell names for the cells used to update the phases.
sub_region	A region name (in the "chrr" column of the seg_table) for a region where the SNP phases and cell major haplotype proportion are updated.

Value

A "rds_list" of the estimated SNP phases (I_hat), estimated cell major haplotype proportion (theta_hat) for all regions.

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