qualityControl {AneuFinder} | R Documentation

## Quality control measures for binned read counts

### Description

Calculate various quality control measures on binned read counts.

### Usage

    qc.spikiness(counts)

    qc.entropy(counts)

    qc.bhattacharyya(hmm)

    qc.sos(hmm)

### Arguments

`counts` | A vector of binned read counts.
`hmm` | An `aneuHMM` object.

### Details

The Shannon entropy is defined as S = - sum( n * log(n) ), where n = counts/sum(counts).
Spikyness is defined as K = sum(abs(diff(counts))) / sum(counts).

### Value

A numeric.

### Functions

- `qc.spikiness`: Calculate the spikiness of a library

- `qc.entropy`: Calculate the Shannon entropy of a library

- `qc.bhattacharyya`: Calculate the Bhattacharyya distance between the '1-somy' and '2-somy' distribution

- `qc.sos`: Sum-of-squares distance from the read counts to the fitted distributions

### Author(s)

Aaron Taudt

[Package AneuFinder version 1.12.1 Index]