# Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

## Documentation for package ‘ACE’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ACE-package | ACE package
ACE | ACE package
ACEcall | Categorize and plot subclonal, single, and double gains / losses
analyzegenomiclocations | Retrieve adjusted copy number information for specific genomic locations
compresstemplate | Reduce the size of a template data frame
copyNumbersSegmented | Segmented data of two tumor samples
correlationmatrix | Create a correlation matrix of all samples in a QDNAseq-object
correlationmatrixadjusted | Create a correlation matrix of all samples in a QDNAseq-object
forcesegmentsontemplate | Custom resegmentation with user-defined segment information
getadjustedsegments | Create a data frame with segment information corresponding to a model
linkvariants | Append columns with total genomic copies and mutant copies to a file with variant/mutation data
loopsquaremodel | Create 'squaremodel' summaries for all samples in a QDNAseq-object
objectsampletotemplate | Converts data of a sample in a QDNAseq-object to a template for ACE functions
ploidyplotloop | Absolute Copy number Estimation
postanalysisloop | Batch analysis of samples in a QDNAseq-object for which models have been chosen
runACE | Absolute Copy number Estimation
segmentstotemplate | Create a template data frame from input that only provides segment information
singlemodel | Calculate potential fits for a single sample
singleplot | Plot an absolute copy number profile for a single sample
squaremodel | Calculate potential fits for a single sample using ploidy as a variable
squaremodelsummary | Create a graphical summary of the result of squaremodel fitting
templatefromequalsegments | Create a template data frame with artificial segments of equal length
twosamplecompare | Overlay copy number data of two samples and compare segment values