All functions
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centromeres.hg19
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location of centromeres at genome build hg19 |
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centromeres.hg38
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location of centromeres at genome build hg38 |
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chromsize.hg19
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chromosome size of genome build hg19 |
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chromsize.hg38
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chromosome size of genome build hg38 |
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cnv_autoCaptureSignatures()
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Auto-capture signature and coresponding exposure |
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cnv_chooseSigNumber()
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Choose optimal number of signatures |
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cnv_derivefeatures()
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Derive copy number feature distributions |
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cnv_extractSignatures()
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Extract signature based on specified rank value |
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cnv_fitMixModels()
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Fit optimal number of mixture model components |
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cnv_generateSbCMatrix()
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Generate a sample-by-component matrix |
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cnv_getLengthFraction()
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Calculate length fraction profile of copy number |
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cnv_pipe()
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CNV signature pipeline |
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cnv_plotDistributionProfile()
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Plot copy number distribution either by length or chromosome |
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cnv_plotFeatureDistribution()
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Plot copy number feature distribution |
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cnv_plotMixComponents()
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Plot mixture fit model components |
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cnv_plotSignatures()
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Plot CNV signatures |
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cnv_quantifySigExposure()
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quantify exposure for samples using Linear Combination Decomposition (LCD) |
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cnv_readprofile()
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Read copy number as a list of data.frame from data.frame or files |