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


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Documentation for package ‘TitanCNA’ version 1.6.0

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TitanCNA-package TITAN: Subclonal copy number and LOH prediction whole genome sequencing of tumours
computeSDbwIndex Compute the S_Dbw Validity Index for 'TitanCNA' model selection
convergeParams TITAN EM trained results for an example dataset
correctReadDepth Correct GC content and mappability biases in sequencing data read counts
data TITAN EM trained results for an example dataset
EMresults TITAN EM trained results for an example dataset
extractAlleleReadCounts Function to extract allele read counts from a sequence alignment (BAM) file
filterData Filter list object based on read depth and missing data
getPositionOverlap Function to assign values to given chromosome-position that overlaps a list of chromosomal segments
loadAlleleCounts Function to load tumour allele counts from a text file or data.frame
loadDefaultParameters Load TITAN parameters
outputModelParameters Formatting and printing 'TitanCNA' results.
outputTitanResults Formatting and printing 'TitanCNA' results.
plotAllelicRatio Plotting functions for 'TitanCNA' results.
plotClonalFrequency Plotting functions for 'TitanCNA' results.
plotCNlogRByChr Plotting functions for 'TitanCNA' results.
plotSubcloneProfiles Plotting functions for 'TitanCNA' results.
runEMclonalCN Function to run the Expectation Maximization Algorithm in 'TitanCNA'.
TitanCNA TITAN: Subclonal copy number and LOH prediction whole genome sequencing of tumours
TitanCNA-dataset TITAN EM trained results for an example dataset
viterbiClonalCN Function to run the Viterbi algorithm for 'TitanCNA'.
wigToRangedData WIG Import Functions