Analysis of Parent-Specific DNA Copy Numbers
The AbstractCBS class
Coerces a DNAcopy object to a CBS object
Gets the table of segments
Gets the table of segments
Coerces a CBS object to a DNAcopy object
Estimate confidence intervals of TCN and DH segment levels
Concatenates segmentation results
Calls segments that are in allelic balance
Calls segments that are in allelic balance
Calls (focal) amplifications
Calls segments that have a neutral total copy number
Calls regions that are copy neutral
Calls gains and losses
Calls segments that are gained, copy neutral, or lost
Calls segments that are in LOH
Calls outliers
Calls segments that are in ROH
Calls/drops single-locus outliers along the genome
The CBS class
Drops zero or more change points
Drops chromosomal regions (a connected set of segments)
Estimate a threshold for calling allelic balance from DH
Estimate a threshold for calling allelic balance from DH
Estimates the length of one total copy-number (TCN) unit
Estimate a threshold for calling LOH from DH
Estimate a threshold for calling LOH from DH
Estimate global background in segmented copy numbers
Estimate global background in segmented copy numbers
Estimates the whole-genome standard deviation of the signals
Gets an example data set
Extract minor and major copy-number mean levels per segment
Extracts segments means at each locus
Extract TCN and DH mean levels per segment
Identifies gaps of a genome where there exist no observations
Call segments to be copy neutral based on allelic imbalance calls and ...
Gets the genomic segments that are complementary to the gaps
Generates original and bootstrapped segment-specific index sets
Calculates various call statistics per chromosome
Gets the set of chromosomes
Calculates the fraction of the genome lost, gained, or aberrant either...
Gets the locus-level data
Gets the name of the sample segmented
Gets the segments
Gets the segments
Gets smoothed locus-level data
Performs a hierarchical clustering of the CN mean levels
Install the DNAcopy package
Joins neighboring segments such that there is no gap in between them
Merge neighboring segments that are not called
Merge a segment and its two flanking segments
Merge two neighboring segments
Merge two neighboring segments
Gets the number of change points
Gets the number of chromosomes
Gets the number of loci
Gets the number of segments
Non-documented objects
The NonPairedPSCBS class
Normalizes copy numbers such that the whole-genome average total copy ...
The PairedPSCBS class
Gets and sets ploidy
Plots the segmentation result along the genome
Plots copy numbers along the genome
Plots parental specific copy numbers along the genome
Prunes the CN profile using dynamical programming
Prunes the CN profile by pruning and merging through hierarchical clus...
Prune the CBS profile by dropping change points that are too small
Package PSCBS
The PSCBS class
Sets and resets the .Random.seed in the global environment
Generates a report of the segmentation results
Reset the segments
Restructuring AbstractCBS objects
Segment genomic signals using the CBS method
Segment total copy numbers and allele B fractions using the Non-paired...
Segment total copy numbers and allele B fractions using the Paired PSC...
Sets the name of the sample segmented
Tests if a segment is in Run-of-Homozygosity (ROH)
Updates the CN mean levels for each segment independently
Updates the CN mean levels jointly in sets of segments
Weighted Quantile Value
Writes the table of segments to file
Writes the table of segments to file
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Useful links