Package: ACE 1.31.0

Jos B Poell

ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.

Authors:Jos B Poell

ACE_1.31.0.tar.gz
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ACE_1.31.0.tgz(r-4.6-any)ACE_1.31.0.tgz(r-4.5-any)
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ACE_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ACE/json (API)
NEWS

# Install 'ACE' in R:
install.packages('ACE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tgac-vumc/ace/issues

Datasets:

On BioConductor:ACE-1.31.0(bioc 3.24)ACE-1.30.0(bioc 3.23)

copynumbervariationdnaseqcoveragewholegenomevisualizationsequencing

7.80 score 20 stars 42 scripts 482 downloads 478 mentions 20 exports 57 dependencies

Last updated from:96f7bbae68. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR168
linux-devel-x86_64NOTE292
source / vignettesOK248
linux-release-x86_64NOTE299
macos-release-arm64NOTE211
macos-oldrel-arm64NOTE127
windows-develNOTE242
windows-releaseNOTE201
windows-oldrelNOTE207
wasm-releaseOK135

Exports:ACEcallanalyzegenomiclocationscompresstemplatecorrelationmatrixcorrelationmatrixadjustedforcesegmentsontemplategetadjustedsegmentslinkvariantsloopsquaremodelobjectsampletotemplateploidyplotlooppostanalysislooprunACEsegmentstotemplatesinglemodelsingleplotsquaremodelsquaremodelsummarytemplatefromequalsegmentstwosamplecompare

Dependencies:BHBiobaseBiocGenericsBiocParallelBiostringsbitopsCGHbaseCGHcallclicodetoolscpp11crayondigestDNAcopyfarverformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggplot2globalsgluegtableimputeIRangesisobandlabelinglambda.rlifecyclelimmalistenvmarraymatrixStatsparallellyQDNAseqR.methodsS3R.ooR.utilsR6RColorBrewerRhtslibrlangRsamtoolsS4VectorsS7scalesSeqinfosnowsnowfallstatmodvctrsviridisLitewithrXVector

ACE vignette

Jos B. Poell

Rendered fromACE_vignette.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2021-01-15
Started: 2018-05-22

Readme and manuals

Help Manual

Help pageTopics
ACE packageACE-package ACE
Categorize and plot subclonal, single, and double gains / lossesACEcall
Retrieve adjusted copy number information for specific genomic locationsanalyzegenomiclocations
Reduce the size of a template data framecompresstemplate
Segmented data of two tumor samplescopyNumbersSegmented
Create a correlation matrix of all samples in a QDNAseq-objectcorrelationmatrix correlationmatrixadjusted
Custom resegmentation with user-defined segment informationforcesegmentsontemplate
Create a data frame with segment information corresponding to a modelgetadjustedsegments
Append columns with total genomic copies and mutant copies to a file with variant/mutation datalinkvariants
Create 'squaremodel' summaries for all samples in a QDNAseq-objectloopsquaremodel
Converts data of a sample in a QDNAseq-object to a template for ACE functionsobjectsampletotemplate
Batch analysis of samples in a QDNAseq-object for which models have been chosenpostanalysisloop
Absolute Copy number Estimationploidyplotloop runACE
Create a template data frame from input that only provides segment informationsegmentstotemplate
Calculate potential fits for a single samplesinglemodel
Plot an absolute copy number profile for a single samplesingleplot
Calculate potential fits for a single sample using ploidy as a variablesquaremodel
Create a graphical summary of the result of squaremodel fittingsquaremodelsummary
Create a template data frame with artificial segments of equal lengthtemplatefromequalsegments
Overlay copy number data of two samples and compare segment valuestwosamplecompare