qualityControl: Quality control measures for binned read counts

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

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

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.