Categorygithub.com/brentp/goleftemdepth
package
0.2.6
Repository: https://github.com/brentp/goleft.git
Documentation: pkg.go.dev
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# README

![GoDoc] (https://godoc.org/github.com/brentp/goleft/emdepth?status.png)

emdepth

-- import "github.com/brentp/goleft/emdepth"

emdepth uses a simplified EM algorithm to assign copy-number given a set of depths. it is based off the implementation in cn.mops. Like cn.mops, it works best with more samples and it assumes that most samples will have copy-number 2. emdepth consists of a single function EMDepth that iteratively assigns depths to copy-numbers, adjusts the center of each copy-number bin. and re-assigns... This package does no normalization and therefore expects incoming data to be normalized.

# Packages

Package mops implements the EM algorithm described in the cn.mops paper.

# Functions

EMDepth returns a slice of integer copy-numbers (CNs) corresponding to the given normalized depths.

# Structs

Cache is a way to track depth states.eps As new items are added to the cache, the value from EMD.Same is compared.
CNV holds the information for a CNV for a single sample.
EMD holds the posterior maximum depth for each copy-number.
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