getQC: Obtain a data.frame with quality metrics
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value Author(s) Examples

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

1	getQC(models)

models

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

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.

A data.frame with columns

Aaron Taudt

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