Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

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Documentation for package ‘ACE’ version 1.25.0

• 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