Man pages for ChristofferFlensburg/superFreq
Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.
| addBindingStrength | Adds binding strength (essentailly same as GC content) to a... |
| analyse | Analyse exomes |
| annotateQ | Run VariantAnnotation on the provided variants |
| annotateSomaticQs | Run VariantAnnotation on the provided samples |
| bamToPileup | Gets pileup from bam over positions. |
| chrLengths | The lengths of the chromsomes |
| chrToX | convert chromsome and position to the single genomic... |
| cohortAnalyseBatch | Analyse individuals for reccuring mutations |
| cohortAnalyseBatchContrast | Analyse individuals for reccuring mutations |
| compareGroups | Compares sets of individuals for reccuring mutations |
| defaultSuperParameters | Returns default parameters |
| defaultSuperRuntimeSettings | Returns default runtime settings |
| defaultSuperSettings | Returns default settings |
| downloadTemplate | Downloads resources and template for a standard analysis |
| dumpInput | internal function for debugging purposes. |
| forceRedoEverything | returns input that uses saved data if present. |
| forceRedoNothing | returns input that uses saved data if present. |
| get104profile | returns the 104 signature from a superFreq q variant object |
| getCohortMutationMatrix | returns relevant mutations in samples in Genes of Interest |
| getCosmicCounts | Retrieves information about cosmic variant IDs |
| getMoreVEPinfo | Import more information about the variants |
| getSettings | Wrapper for getting settings, containing defaults for missing... |
| getStories | Combines variants and CNAs to clonal evolution |
| getVariantsByIndividual | Quality controls the variants in the vcfs, using the bams. |
| importCaptureRegions | Imports capture regions from a bed file with GC information. |
| importSampleMetaData | Imports metadata about the samples |
| loadData | Loads saved data |
| makeFitPlots | Plots results from differential coverage analysis |
| makeHeatmap | plots a heatmap |
| makepHeatmap | plots a heatmap |
| mcri | Turns colours into similar colours from the Murdoch Childrens... |
| mergeBatches | Merges data from several batches for cohort analysis |
| moreVEPnames | internal function |
| plotCNAheatmapOverGoI | plots a heatmap of copy numbers, focusing on a gene of... |
| plotCNAheatmapWithGoI | plots a heatmap of copy numbers, highlighting genes of... |
| plotCohortMutationHeatmap | plots mutations in samples in Genes of Interest |
| plotColourScatter | A better version of plot |
| plotCR | plots a copy number profile |
| plotMA | a plotting function for MA plots. |
| plotRiver | plots a river plot |
| plotStories | plots line plots of clonalities |
| postAnalyseVEP | Runs VEP on a R and plot directory that superFreq has been... |
| printHTML | generates an HTML to navigate superFreq output |
| qToGRanges | Transforms a variant q data frame into granges |
| qualityScatter | plots a scatter of the VAF between two samples |
| requireFileExists | checks if a file exists, and creates an error if it doesnt. |
| runDE | Run differential coverage analysis. |
| runSummaryPostAnalysis | runs analyses across all samples in the batch |
| runVEP | Run VEP on the provided variants |
| severityToType | The variant effect as function of severity |
| superCohort | looks for reccuring events across all individuals in a batch... |
| superFreq | Wrapper to run default superFreq analysis |
| superInputFiles | sets up and checks the input files for superFreq |
| superOutputDirectories | Sets up and checks the output directories. |
| superVersion | Return the current version of superFreq. |
| typeToSeverity | Ranks the variant effects |
| VAconsequenceToSeverityRank | coding' is used by the location run to cover all the coding... |
| vafScatter | plots a scatter of the VAF between two samples |
| VAseverityToConsequence | coding' is used by the location run to cover all the coding... |
| writeToVCF | exports variants to VCF |
| xToChr | Extract chromsome of genomic coordinate |
| xToGene | find the gene closest to the genomic coordinate x |
| xToPos | Extract position of genomic coordinate |
