Package: ACE 1.23.0

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_1.23.0.tar.gz
ACE_1.23.0.zip(r-4.5)ACE_1.23.0.zip(r-4.4)ACE_1.23.0.zip(r-4.3)
ACE_1.23.0.tgz(r-4.4-any)ACE_1.23.0.tgz(r-4.3-any)
ACE_1.23.0.tar.gz(r-4.5-noble)ACE_1.23.0.tar.gz(r-4.4-noble)
ACE_1.23.0.tgz(r-4.4-emscripten)ACE_1.23.0.tgz(r-4.3-emscripten)
ACE.pdf |ACE.html✨
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:

copyNumbersSegmented - Segmented data of two tumor samples

On BioConductor:ACE-1.23.0(bioc 3.20)ACE-1.22.0(bioc 3.19)

bioconductor-package

20 exports 0.71 score 78 dependencies 478 mentions

Last updated 2 months agofrom:123601aa8f

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

Dependencies:askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops CGHbase CGHcall cli codetools colorspace cpp11 crayon curl digest DNAcopy fansi farver formatR futile.logger futile.options future future.apply GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue gtable httr impute IRanges isoband jsonlite labeling lambda.r lattice lifecycle limma listenv magrittr marray MASS Matrix matrixStats mgcv mime munsell nlme openssl parallelly pillar pkgconfig QDNAseq R.methodsS3 R.oo R.utils R6 RColorBrewer Rhtslib rlang Rsamtools S4Vectors scales snow snowfall statmod sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

ACE vignette

Jos B. Poell

Rendered fromACE_vignette.Rmdusingknitr::rmarkdownon Jun 13 2024.

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