Function to format TitanCNA results in to a data.frame and output the results to a tab-delimited file.
● Data Source:
BioConductor
● Keywords: IO, manip
● Alias: outputModelParameters, outputTitanResults
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TITAN is a software tool for inferring subclonal copy number alterations (CNA) and loss of heterozygosity (LOH). The algorithm also infers clonal group cluster membership for each event and the tumour proportion, or cellular prevalence, for each event.
● Data Source:
BioConductor
● Keywords: IO, manip, package
● Alias: TitanCNA, TitanCNA-package
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Three plotting functions for TitanCNA results. plotCNlogRByChr plots the copy number results from log ratio data. plotAllelicRatio plots the allelic imbalance and loss of heterozygosity (LOH) from allelic ratio data. plotClonalFrequency plots the clonal cluster and cellular prevalence results for each data point.
● Data Source:
BioConductor
● Keywords: aplot, color
● Alias: plotAllelicRatio, plotCNlogRByChr, plotClonalFrequency, plotSubcloneProfiles
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Compute the S_Dbw Validity Index internal cluster validation from the TitanCNA results to use for model selection.
● Data Source:
BioConductor
● Keywords: manip
● Alias: computeSDbwIndex
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Correct GC content and mappability biases in tumour sequence read counts using Loess curve fitting. Wrapper for function in HMMcopy.
● Data Source:
BioConductor
● Keywords: IO, manip
● Alias: correctReadDepth
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Function to extract allele read counts from a sequence alignment (BAM) file at specific positions of interest. The positions are passed in as the file path to a file in variant call format (VCF).
● Data Source:
BioConductor
● Keywords: IO
● Alias: extractAlleleReadCounts
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Filters all vectors in list based on specified chromosome(s) of interest, minimum and maximum read depths, missing data, mappability score threshold
● Data Source:
BioConductor
● Keywords: manip
● Alias: filterData
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Given a list of chromosomes and positions, uses a C-based function that searches a list of segments to find the overlapping segment. Then, takes the value (4th column in segment data.frame) of the overlapping segment and assigns to the given chromosome and position.
● Data Source:
BioConductor
● Keywords: manip
● Alias: getPositionOverlap
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Function to load in the allele counts from tumour sequencing data from a delimited text file or data.frame object.
● Data Source:
BioConductor
● Keywords: IO
● Alias: loadAlleleCounts
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Load TITAN model parameters based on maximum copy number and number of clonal clusters.
● Data Source:
BioConductor
● Keywords: attribute
● Alias: loadDefaultParameters
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