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