Calculate and make a quality call for relative copy number profiles

Function to classify the quality of relative copy number profile calls from QDNAseq or WiseCondorX.

Usage

GetSampleQualityDecision(x, metric = "quantile", cutoff = 0.95)

Arguments

x

QDNASeq object containing the relative copy number calls as well as the segmented relative copy number calls.

metric

The metric to use for determining quality. Either 'quantile' or 'DecisionTree'.

cutoff

The cutoff to use for quantile-based quality filtering. Not applicable when the metric is 'DecisionTree'.

Value

A dataframe of sample quality decisions ("Low" or "High" quality sample)

Details

Expects the input of a QDNAseq object containing relative copy-number calls (such as from QDNASeq or WiseCondorX).
Classifies relative copy number profiles as "High" or "Low" quality.