find_clone: Identify clones in hierarchical tree.

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

Identify clones in hierarchical tree.

Description

Based on hierarchical clustering, identify the hard/soft clones.

Usage

find_clone(hc, fdr_thresh = -2, share_min = 0.9, n_share = 3,
  bymax = TRUE, climb_from_size = 2, climb_to_share = 3, graphic = TRUE)

Arguments

hc	The hclust objects with new items added generated by hclust_tree.
fdr_thresh	FDR criterion for clone nodes. Default: -2.
share_min	A feature is considered shared if present in share_min fraction of leaves in a node.Default: 0.90.
n_share	Minimal number of shared features in a clone node. Default: 3.
bymax	Logical. If TRUE (Default), use maximal of mean FDR for the node to find clones.
climb_from_size	An integer.
climb_to_share	An integer.
graphic	Logical. If TRUE (Default), generate the hierarchical tree plot with hard/soft clones labeled.

Value

A hclust object.

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