plot_scATAC_cnv: Generate Alleloscope object for analysis

Description Usage Arguments Value

View source: R/plot_scATAC_cnv.R

Description

Generate Alleloscope object for analysis

Usage

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