plot_scATAC_cnv: Generate Alleloscope object for analysis

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

Generate Alleloscope object for analysis

Description

Generate Alleloscope object for analysis

Usage

plot_scATAC_cnv(
  raw_mat = NULL,
  cell_type = NULL,
  normal_lab = "normal",
  size = NULL,
  window_w = 1e+07,
  window_step = 2e+06,
  plot_path = NULL,
  nclust = 3,
  var.filter = FALSE
)

Arguments

raw_mat	A binned coverage matrix (m1 bin by n1 cell) with values being read counts for scATAC-seq of tumor sample (with some normal cells). The matrix can be generated using https://github.com/seasoncloud/Basic_CNV_SNV/blob/main/scripts/Gen_bin_cell_atac.R
cell_type	A matrix with two columns: COL1- cell barcodes; COL2- cell types (Tumor cells should be labeled with "tumor1, tumor2 and etc.").
normal_lab	Character(s) indicating the cell types considered as normal cells. If not specify, "normal" cell type should exist in the cell_type dataframe.
size	A matrix with two columns: col1: different chromosome; col2: for the size (bp) of different chromosomes (eq.1-22).
window_w	window size for signal pooling in individual cells.
window_step	step size for signal smoothing in individual cells.
plot_path	Path to plot the heatmap.
nclust	Integer. Number of clusters the rows are divided into for visualization and clustering.
var.filter	Logical (TRUE/FALSE) Whether or not to filter our highly variable features.

Value

A vector indicating the ordered cluster number (from hierarchical clustering) of each cell and a heatmap saved.

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