getQC: Obtain a data.frame with quality metrics

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

Obtain a data.frame with quality metrics

Description

Obtain a data.frame with quality metrics from a list of aneuHMM objects or a list of files that contain such objects.

Usage

getQC(models)

Arguments

models

A list of GRanges-class or aneuHMM objects or a character vector with files that contain such objects.

Details

The employed quality measures are:

• total.read.count: Total read count.

• avg.binsize: Average binsize.

• avg.read.count: Average read count.

• spikiness: Bin-to-bin variability of read count.

• entropy: Shannon entropy of read counts.

• complexity: Library complexity approximated with a Michaelis-Menten curve.

• loglik: Loglikelihood of the Hidden Markov Model.

• num.segments: Number of copy number segments that have been found.

• bhattacharrya distance: Bhattacharyya distance between 1-somy and 2-somy distributions.

• sos: Sum-of-squares distance of read counts to the fitted distributions in their respective segments.

Value

A data.frame with columns

Author(s)

Aaron Taudt

Examples

## Get a list of HMMs
folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
files <- list.files(folder, full.names=TRUE)
df <- getQC(files)

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