Select_normal: Identify candidate normal cells and normal regions for cell...

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

Identify candidate normal cells and normal regions for cell coverage normalization

Description

Identify candidate normal cells and normal regions for cell coverage normalization

Usage

Select_normal(
  Obj_filtered = NULL,
  raw_counts = NULL,
  cell_nclust = 5,
  plot_theta = FALSE,
  pre_sel = FALSE,
  cell_type = NULL,
  cutree_rows = 3,
  mincell = NULL
)

Arguments

Obj_filtered	An Alleloscope object with major haplotype proportion (theta_hat) for each cell of each region in the "rds_list".
raw_counts	A large binned coverage matrix (bin by cell) with values being read counts for all chromosomal regions of tumor sample.
cell_nclust	Integer. Number of clusters used in identifying normal cells in the sample.
plot_theta	Logical (TRUE/FALSE). Whether or not to plot the hierarchical clustering result using the theta_hat values across regions.
pre_sel	Logical (TRUE/FALSE). Whether or not to use theta_hat from regions without segmentation (each chromosome) to identify normal cells for segmentation.
cell_type	A matrix with two columns: COL1- cell barcodes; COL2- cell types ("tumor" and others)
cutree_rows	Integer. Number of clusters the rows are divided into for visualization (inherited from the pheatmap function).
mincell	An integer to filter out regions with minimum number of cells.

Value

A Alleloscope object with a "select_normal" list added. A "select_normal" list includes "barcode_normal": Barcodes of the identified normal cells in the tumor sample. "region_normal": A vector of ordered potential normal regions for selection. (1st is the most possible.) "region_normal_rank": A table with the potential "normal regions" for the k clusters from hierarchical clustering. "k_normal": An integer indicates the kth clsuter that is idenfied as "normal cells"

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