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

Description Usage Arguments Value

View source: R/Est_regions.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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 June 18, 2021, 7:24 p.m.