ACE-package: ACE package

In tgac-vumc/ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

ACE package

Description

ACE is developed to analyze (low-coverage) whole genome sequencing data, infer absolute copies of chromosomal segments, estimate tumor cell percentage, and create visually appealing and highly interpretable copy number profiles. For preprocessing it utilizes the QDNAseq package, but in principle any segmented copy number data can be used. The core function, runACE, performs the whole pipeline from mapped reads to suggested copy number profiles. Functions such as singlemodel and singleplot enable further inspection and customization of individual samples. For further instructions, please consult the vignette for a walkthrough, or the individual function documentation for detailed function specifics.

Details

ACE basically starts from segmented copy number data. To arrive at this point from mapped sequencing reads, it runs a set of default QDNAseq functions to obtain QDNAseqCopyNumbers objects with segmented data. For copy number plots, ACE uses ggplot2. The following functions comprise the main functionality of ACE:

runACE

Perform model fitting on all samples in a directory

singlemodel

Perform model fitting on a single sample

singleplot

Create an absolute copy number plot of a single sample

squaremodel

Perform model fitting on a single sample using both cellularity and ploidy as variable

getadjustedsegments

Use obtained model parameters to calculate adjusted segment values

linkvariants

Link variant data to copy number data to estimate the number of mutant copies

analyzegenomiclocations

Look up adjusted segment values of specific genomic locations

postanalysisloop

Use obtained model parameters for all samples in a QDNAseq-object to print final output, e.g. copy number plots, adjusted segment data, mutation data linked to adjusted copy number data

The following functions provide some more "niche" functionality

ACEcall

Call losses and gains for all segments and visualize in copy number profile

twosamplecompare

Compare segments and copy number profile of two samples and plot overlay

squaremodelsummary

Return or print a summary of a squaremodel

loopsquaremodel

Perform squaremodel fitting on all samples in a QDNAseq-object

forcesegmentsontemplate

Custom resegmentation with user-defined segment information

License

This package is licensed under GPL.

Author(s)

Jos B. Poell

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.