Man pages for J0bbie/R2CPCT
Misc. functions to perform import and analysis of WGS and RNA-Seq samples
| cleanSeqlevels | Cleans and standardizes chromosomal information. |
| detectEnrichmentOfMutants | Perform a Fisher's Exact test to detect groups enriched with... |
| detectKataegis_OLD | Detect kataegis-like events by using a PCF algorithm. |
| determineMutationalBurden | Determine the mutational burden of the CPCT-02/HMF samples. |
| determineTiTv | Determine the number of Ti and Tv contexts and Ti/Tv ratio... |
| driverList | See misc/generateDriverList.R |
| findCPCTCenter | Find corresponding center based on CPCT number. |
| fitCustomMutSigs | Performs mutational signature fitting against a pre-defined... |
| fitMutSigs | Performs optimal fitting of the contribution of mutational... |
| GENCODE.v38 | # Import GENCODE v38 annotation. GENCODE.v38.GTF <-... |
| GENCODE.v38.Exons | GENCODE.v38.GTF <-... |
| generateCombinedReport | Generate a gene-level overview of all overlapping mutations... |
| importArriba | Import Arriba results. |
| importdriverCatalogHMF | Import the driver catalog as determined by HMF. |
| importGISTIC2 | Imports the GISTIC2 recurrent peak and chromosomal arms... |
| importLINXFusions | Import detected fusions by LINX. |
| importPurityStatsPURPLE | Import the driver catalog as determined by HMF. |
| importSomaticCopynumberPURPLE | Import the somatic CNV segments as estimated by PURPLE. |
| importSomaticVariantsVEP | Import VEP-annotated VCF files obtained from HMF... |
| importStructuralVariantsPURPLE | Import the somatic structural variants as estimated by GRIDSS... |
| importWGSOfCohort | Imports all the WGS data of multiple samples (cohort). |
| importWGSOfSample | Imports all the WGS data of a single CPCT-02 sample. |
| initializeLogger | Initialize a parallel-ready logger. |
| makeOncoplot.CPCT | Generates a mutational signature plot. |
| memoSort | Sorting function based on mut. exclusivity. |
| performCHORD | Performs CHORD analysis. |
| performGISTIC2 | Detect genes under selection by focal amplification/deletion... |
| performLINX | Run LINX on one or multiple samples to discover fusion and... |
| performShatterSeek | Performs ShatterSeek analysis. |
| plotMutationalSignaturesCOSMIC | Generates a mutational signature plot (COSMIC signatures). |
| plotMutationalSignaturesCustom | Generates a mutational signature plot for custom signatures. |
| plotOverviewGISTIC2 | Generates an overview of the GISTIC2 copy-number landscape. |
| proposedAetiologyCOSMICv3.2 | library(rvest) |
| proteinDomains | # Import protein domains from PROT2HG ——— |
| retrieveDESeq2Results | Retrieve the results from a DESeq2-analysis using IHW and LFC... |
| retrieveFilesWGS | Retrieves the WGS files needed for analysis into the same... |
| runArriba | Run Arriba on RNA-Seq samples using structural-variants... |
| rundNdS | Perform dN/dS analysis on a set of mutations from multiple... |
