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 |