Man pages for afrangou/CleanCNA
Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.
| AssessBBDPCRun | Assess whether the sample passes based on the output of... |
| AssessBBDPCRun_afterpeakcalling | Assess BBDPC run after peak calling |
| AssessBBDPCRun_B | Assess success of Battenberg CNV call using subclones file... |
| call.peaks | Call peaks from density and return dataframe with x,y... |
| CleanBedopsOutput | Clean bedops output |
| CNAsDriversComplexHeatmap | Heatmap to show CNA status in a set of driver genes across a... |
| CNAsDriversHeatmapDendrogram | Heatmap to show CNA status in a set of driver genes across a... |
| CodeSegments | Code all segments in all samples in the cohort |
| CodeSegments_test | Code all segments in all samples in the cohort |
| CollateSubclones | Collate all segments in all samples in the cohort |
| computed.expected.peak.loc | Computes an expected VAF peak given a given purity and ploidy |
| ComputePeaksVAF | Compute new purity estimate based on VAF peaks at particular... |
| ComputePeaksVAF_nf | Compute Peaks VAF (for nf) |
| ConvertImputeInputToBeagleInput | Convert Impute2 input to Beagle5 input |
| convertSubclonesSingleSample | Converts hg37 output subclones files to hg38 using reference... |
| CreateScriptsDirs | Make scripts for all Battenberg and DPClust runs with options... |
| CreateScriptsDirsBeagle | Create all scripts and dirs required for a set of samples,... |
| CreateScriptsDirsFixedParams | Creates scripts and directories given a fixed purity (rho)... |
| CreateWGDScriptDirs | Create scripts and directories for a sample wanting an... |
| FirstBB | Make scripts for all Battenberg and DPClust runs with options... |
| GenerateDPinput | function to make the DPinput file for input into DPClust |
| GenerateDPinput_mutect_vcf | Generate DP input |
| GenerateDPinput_strelka_vcf | Generate DP input for strelka vcfs, using tier 1 snvs |
| GenerateDPinput_t2BamAC | Generates DPinput files using t2BamAC column with Dan's... |
| GenerateDPinput_t2BamAC_Beagle | Generate DPinput file using t2BamAC column of filtered vcf,... |
| GenerateDPinput_t2BamAC_Beagle_nf | Generate DP input (for Beagle, in Nextflow context) |
| GenerateDPinputt2BamAC_Beagle_nf | Generate DP input (for Beagle, in Nextflow context) |
| GenomewideStackedBar | Prep data for genome wide stacked barplot Create stacked bar... |
| GenomewideStackedBarPlot | Create stacked bar plot |
| LabelGenomecov | Collate all segments in all samples in the cohort |
| PassFail | function producing an indicator file which states whether the... |
| PrepDataForSummary | Make summary table with filepaths for required files... |
| PrepShapeIt2 | Make an input file for ShapeIt2 for a tumour sample. |
| QualityControl_CNAqc | Quality Control using BB, DPC, VAFpeaks (CNAqc) calls |
| read.segs | Read subclones file from CallSubclones function from... |
| read.snvs | Reads SNV file for peak calling |
| reestimate.purity | Reestimate the sample purity for a given karyotype |
| RunBeagle5 | Run Beagle 5 |
| RunDPClust_Beagle_nf | Runs DPClust using input provided in... |
| RunShapeIt2 | Run ShapeIt2 |
| SetUpRun2BBDPC | Recalculate purity and ploidy based on clonal cluster for a... |
| WriteBeagleAsImpute | Write Beagle as Impute |
