ACE-package {ACE} | R Documentation

## 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

[Package ACE version 1.12.0 Index]