getQC {AneuFinder} | R Documentation

## 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)

[Package AneuFinder version 1.12.1 Index]