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. |
removeEmptyClusters |
Post-process TitanCNA results by removing clusters with proportion of data points altered lower than a threshold. The number of clonal clusters, cellular prevalence, and normal contamination will be adjusted to reflect the remaining clonal clusters. |
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 |