cbs.segment_all: Generate the segmented profile for each cell.

In ananjysong/SCclust: Single Cell Copy Number Analysis and Clustering

Generate the segmented profile for each cell.

Description

Generate the segmented profile for each cell in the input directory with CBS. (Including GC correction)

Usage

cbs.segment_all(input_file_dir, Nk = "5k", gc, alpha, nperm, undo.SD,
  min.width, method = "multiplier", genome = "hg")

Arguments

input_file_dir	The directory that contains the bin count files for all cells. For example, one bin count file for a cell is CJA1023.varbin.20k.txt
Nk	Default value: 5k. It denotes the number of bins. 5000 = 5k, 10000 = 10k, ...
gc	The GC content table.
alpha	Parameter alpha defined in DNAcopy package.
nperm	Parameter nperm defined in DNAcopy package.
undo.SD	Parameter undo.SD defined in DNAcopy package.
min.width	Parameter min.width defined in DNAcopy package.
method	Default: "multiplier" to transform the ratio data to integer CN state. When genome is hg-dm hybrid, set method as "dmploidies" to use dm plodies as reference.
genome	Default: "hg" (Human genome). hg-dm hybrid genome: "hgdm".

Value

The list containing seg.quantal and ratio.quantal matrix for all cells in the input_file_dir.

ananjysong/SCclust documentation built on April 18, 2022, 10:06 p.m.