Man pages for ATLi2001/titancna
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
| computeSDbwIndex | Compute the S_Dbw Validity Index for 'TitanCNA' model... |
| correctCN | Compute purity and ploidy corrected log ratios; recompute... |
| correctReadDepth | Correct GC content and mappability biases in sequencing data... |
| filterData | Filter list object based on read depth and missing data and... |
| getPositionOverlap | Function to assign values to given chromosome-position that... |
| haplotype | Function to load tumour allele counts from a text file or... |
| loadAlleleCounts | Function to load tumour allele counts from a text file or... |
| loadDefaultParameters | Load TITAN parameters |
| runEMclonalCN | Function to run the Expectation Maximization Algorithm in... |
| TitanCNA-dataset | TITAN EM trained results for an example dataset |
| TitanCNA-output | Formatting and printing 'TitanCNA' results. |
| TitanCNA-package | TITAN: Subclonal copy number and LOH prediction whole genome... |
| TitanCNA-plotting | Plotting functions for 'TitanCNA' results. |
| viterbiClonalCN | Function to run the Viterbi algorithm for 'TitanCNA'. |
| wigToRangedData | WIG Import Functions |
