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✨
DESCRIPTION |NEWS
card.svg |card.png
ACE/json (API)

# 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:

copyNumbersSegmented - Segmented data of two tumor samples

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

copynumbervariation dnaseq coverage wholegenome visualization sequencing

7.87 score 21 stars 47 scripts 462 downloads 478 mentions 20 exports 57 dependencies

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

Target	Result	Time
bioc-checks	ERROR	168
linux-devel-x86_64	NOTE	304
source / vignettes	OK	228
linux-release-x86_64	NOTE	269
macos-release-arm64	NOTE	169
macos-oldrel-arm64	NOTE	167
windows-devel	NOTE	290
windows-release	NOTE	478
windows-oldrel	NOTE	207
wasm-release	OK	141

Exports:ACEcall analyzegenomiclocations compresstemplate correlationmatrix correlationmatrixadjusted forcesegmentsontemplate getadjustedsegments linkvariants loopsquaremodel objectsampletotemplate ploidyplotloop postanalysisloop runACE segmentstotemplate singlemodel singleplot squaremodel squaremodelsummary templatefromequalsegments twosamplecompare

Dependencies:BH Biobase BiocGenerics BiocParallel Biostrings bitops CGHbase CGHcall cli codetools cpp11 crayon digest DNAcopy farver formatR futile.logger futile.options future future.apply generics GenomicRanges ggplot2 globals glue gtable impute IRanges isoband labeling lambda.r lifecycle limma listenv marray matrixStats parallelly QDNAseq R.methodsS3 R.oo R.utils R6 RColorBrewer Rhtslib rlang Rsamtools S4Vectors S7 scales Seqinfo snow snowfall statmod vctrs viridisLite withr XVector

ACE vignette

Rendered fromACE_vignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

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