A parent class for containers of QDNAseq data
Adds phenotype data from a file to a QDNAseqReadCounts or a QDNAseqCopyNumbers object
Adjusts the filtering on which bins are used
Calculate binned read counts from a set of BAM files
Call aberrations from segmented copy number data
Divide binned read counts with those of reference samples
Correct binned read counts for GC content and mappability
Builds bin annotation data for a particular bin size
Estimate correction to read counts for GC content and mappability
Gets bin annotation data for a particular bin size
Highlights data points in a plotted profile to evaluate filtering
Plot median read counts as a function of GC content and mappability
Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object
Plot noise as a function of sequence depth