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 |
correctIntegerCN |
Compute purity and ploidy corrected log ratios; recompute integer CN for high-level amplifications. |
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 |
filterData |
Filter list object based on read depth and missing data and returns a filtered data.table object. |
getHaplotypesFromVCF |
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') |
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 and returns a data.table. |
loadBXcountsFromBEDDir |
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') |
loadDefaultParameters |
Load TITAN parameters |
loadHaplotypeAlleleCounts |
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') |
outputModelParameters |
Formatting and printing 'TitanCNA' results. |
outputTitanResults |
Formatting and printing 'TitanCNA' results. |
outputTitanSegments |
Formatting and printing 'TitanCNA' results. |
plotAllelicRatio |
Plotting functions for 'TitanCNA' results. |
plotClonalFrequency |
Plotting functions for 'TitanCNA' results. |
plotCNlogRByChr |
Plotting functions for 'TitanCNA' results. |
plotHaplotypeFraction |
Plotting functions for 'TitanCNA' results. |
plotSegmentMedians |
Plotting functions for 'TitanCNA' results. |
plotSubcloneProfiles |
Plotting functions for 'TitanCNA' results. |
runEMclonalCN |
Function to run the Expectation Maximization Algorithm in 'TitanCNA'. |
setGenomeStyle |
Function to load tumour allele counts from a text file or data.frame and returns a data.table. |
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'. |
wigToGRanges |
WIG Import Functions. wigToGRanges (new) and wigToRangedData (deprecated) |
wigToRangedData |
WIG Import Functions. wigToGRanges (new) and wigToRangedData (deprecated) |