Package: TitanCNA 1.45.0

Gavin Ha

TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Authors:Gavin Ha

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TitanCNA.pdf |TitanCNA.html✨
TitanCNA/json (API)
NEWS

# Install 'TitanCNA' in R:

install.packages('TitanCNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gavinha/titancna/issues

Datasets:

convergeParams - TITAN EM trained results for an example dataset
data - TITAN EM trained results for an example dataset

On BioConductor:TitanCNA-1.45.0(bioc 3.21)TitanCNA-1.44.0(bioc 3.20)

sequencing wholegenome dnaseq exomeseq statisticalmethod copynumbervariation hiddenmarkovmodel genetics genomicvariation immunooncology 10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity

8.45 score 94 stars 67 scripts 268 downloads 5 mentions 25 exports 82 dependencies

Last updated 2 months agofrom:19f37d42da. Checks:OK: 1 ERROR: 2 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win-x86_64	ERROR	Dec 19 2024
R-4.5-linux-x86_64	ERROR	Dec 19 2024
R-4.4-win-x86_64	WARNING	Dec 19 2024
R-4.4-mac-x86_64	WARNING	Dec 19 2024
R-4.4-mac-aarch64	WARNING	Dec 19 2024
R-4.3-win-x86_64	WARNING	Dec 19 2024
R-4.3-mac-x86_64	WARNING	Dec 19 2024
R-4.3-mac-aarch64	WARNING	Dec 19 2024

Exports:computeSDbwIndex correctIntegerCN correctReadDepth filterData getHaplotypesFromVCF getPositionOverlap loadAlleleCounts loadBXcountsFromBEDDir loadDefaultParameters loadHaplotypeAlleleCounts outputModelParameters outputTitanResults outputTitanSegments plotAllelicRatio plotClonalFrequency plotCNlogRByChr plotHaplotypeFraction plotIdiogram.hg38 plotSegmentMedians plotSubcloneProfiles runEMclonalCN setGenomeStyle viterbiClonalCN wigToGRanges wigToRangedData

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray dplyr fansi fastmap foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml zlibbioc

TitanCNA

Rendered fromTitanCNA.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2019-05-30
Started: 2015-01-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TITAN: Subclonal copy number and LOH prediction whole genome sequencing of tumours	TitanCNA-package TitanCNA
Compute the S_Dbw Validity Index for 'TitanCNA' model selection	computeSDbwIndex
Compute purity and ploidy corrected log ratios; recompute integer CN for high-level amplifications.	correctIntegerCN
Correct GC content and mappability biases in sequencing data read counts	correctReadDepth
Filter list object based on read depth and missing data and returns a filtered data.table object.	filterData
Function to assign values to given chromosome-position that overlaps a list of chromosomal segments	getPositionOverlap
Function to load tumour allele counts from a text file or data.frame and returns a data.table ('loadHaplotypeAlleleCounts'). Function to load phased heterozygous sites from a VCF file ('getHaplotypesFromVCF')	getHaplotypesFromVCF loadBXcountsFromBEDDir loadHaplotypeAlleleCounts
Function to load tumour allele counts from a text file or data.frame and returns a data.table.	loadAlleleCounts setGenomeStyle
Load TITAN parameters	loadDefaultParameters
Formatting and printing 'TitanCNA' results.	outputModelParameters outputTitanResults outputTitanSegments
Plotting functions for 'TitanCNA' results.	plotAllelicRatio plotClonalFrequency plotCNlogRByChr plotHaplotypeFraction plotSegmentMedians plotSubcloneProfiles
Function to run the Expectation Maximization Algorithm in 'TitanCNA'.	runEMclonalCN
TITAN EM trained results for an example dataset	convergeParams data EMresults TitanCNA-dataset
Function to run the Viterbi algorithm for 'TitanCNA'.	viterbiClonalCN
WIG Import Functions. wigToGRanges (new) and wigToRangedData (deprecated)	wigToGRanges wigToRangedData