Man pages for acc-bioinfo/TMBleR
Tumor Mutational Burden Quantification From Gene Panels And WES
| annotateTMB | Annotate TMB dataframe with clinical outcome |
| applyFilters | Apply filters on a list of CollapsedVCF objects |
| applySimulatePanel | Downsample a whole exome sequencing (WES) dataset to a subset... |
| applyTMB | Provide text and graphical output for Tumor Mutational Burden... |
| callFilters | Filters variants according to input arguments |
| callTMB | Perform Tumor Mutational Burden (TMB) quantification |
| compareROC | Generate and compare two ROC curves of TMB performance in... |
| compareTMBdistribution | Compare TMB distribution in responders and nonresponders |
| correlateTMBvalues | Correlate panel-based TMB values with WES-based TMB values |
| COSMIC_hg19_demo | Cosmic coding mutations hg19 |
| COSMIC_hg38_demo | Cosmic coding mutations hg38 |
| dot-fetch_filtered_SNV | .fetch_filtered_SNV |
| dot-remove_noncoding_SNV | .remove_noncoding_SNV |
| ExamplePaneldesign | Dataset containing sequencing design of a panel |
| ExampleWESdesign | Dataset containing sequencing design of a WES experiment |
| ExampleWESvcfs | Dataset containing example vcf from WES |
| filterByVAF | Filter variants according to variant allele frequency |
| filterCOSMIC | Filter variants described in COSMIC |
| filterTruncatingTumorSuppr | Filter truncating variants in tumor suppressors |
| filterVariantType | Filter variants by the specified type |
| formatCOSMIC | Read in a COSMIC file and format it for usage in TMBleR |
| generateBoxplot | Generate boxplots of TMB distribution versus clinical... |
| generateROC | Generate ROC curves to evaluate TMB performance in... |
| Hellman_SimulatedFM1Panel_WES | Dataset containing tumor mutational burden and clinical data... |
| HumanTumorSuppressors | List of human tumor suppressors |
| inputToTMB | Provide a suitable input to the callTMB function for TMB... |
| plotTMB | Plots Tumor Mutational Burden (TMB) |
| readDesign | Read design file |
| readVcfFiles | Read VCF files |
| removeCancerVariants | Remove cancer variants |
| simulatePanel | Downsample a whole exome sequencing (WES) dataset to a subset... |
| TMB_Horizon | Input to the plotTMB function to be used in tests |
| TMBs_SimulatedPanel | Panel-based TMB to use as input to the correlateTMBvalues and... |
| TMBs_WES | WES-based TMB to use as input to the correlateTMBvalues and... |
| TMB_VanAllen | Input to the plotTMB function to be used in tests |
| VanAllen_Clinical | Dataset containing tumor mutational burden and clinical data... |
| vcfs_all | Data to use as input to the applyTMB functions in tests |
| vcfs_NoCancer_ForPanel | Data to use as input to the applySimulatedPanel function in... |
