cbs.segment_one: Segment the normalzied bin count profile for individual cell...

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

Segment the normalzied bin count profile for individual cell for GC content.

Description

Generate the segmented profile for individual cell with CBS.

Usage

cbs.segment_one(bin_mat, alpha, nperm, undo.SD, min.width,
  method = "multiplier", genome = "hg", graphic = TRUE)

Arguments

bin_mat	The normalized bin count files generated by gc_one.
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".
graphic	Default: TRUE. Generate the copy number profile plot.

Value

The segmented profile for individual cell

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