Man pages for tgac-vumc/ACE
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

ACEcallCategorize and plot subclonal, single, and double gains /...
ACE-packageACE package
analyzegenomiclocationsRetrieve adjusted copy number information for specific...
compresstemplateReduce the size of a template data frame
copyNumbersSegmentedSegmented data of two tumor samples
correlationmatrixCreate a correlation matrix of all samples in a...
forcesegmentsontemplateCustom resegmentation with user-defined segment information
getadjustedsegmentsCreate a data frame with segment information corresponding to...
linkvariantsAppend columns with total genomic copies and mutant copies to...
loopsquaremodelCreate 'squaremodel' summaries for all samples in a...
objectsampletotemplateConverts data of a sample in a QDNAseq-object to a template...
postanalysisloopBatch analysis of samples in a QDNAseq-object for which...
runACEAbsolute Copy number Estimation
segmentstotemplateCreate a template data frame from input that only provides...
singlemodelCalculate potential fits for a single sample
singleplotPlot an absolute copy number profile for a single sample
squaremodelCalculate potential fits for a single sample using ploidy as...
squaremodelsummaryCreate a graphical summary of the result of squaremodel...
templatefromequalsegmentsCreate a template data frame with artificial segments of...
twosamplecompareOverlay copy number data of two samples and compare segment...
tgac-vumc/ACE documentation built on Nov. 15, 2018, 5:39 p.m.