getQC {AneuFinder} | R Documentation |
Obtain a data.frame with quality metrics from a list of aneuHMM
objects or a list of files that contain such objects.
getQC(models)
models |
A list of |
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)