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| GenVisR-package | GenVisR |
| .getData_Lolliplot | Method getData |
| .getData_MutSpectra | Method getData |
| .getData_Rainfall | Method getData |
| .getData_waterfall | Method getData |
| brcaMAF | Truncated BRCA MAF file |
| Clinical | Class Clinical |
| Clinical-class | Class Clinical |
| cnFreq | Construct copy-number frequency plot |
| cnSpec | Construct copy-number cohort plot |
| cnView | Construct copy-number single sample plot |
| compIdent | Construct identity snp comparison plot |
| covBars | Construct an overall coverage cohort plot |
| cytoGeno | Cytogenetic banding dataset |
| drawPlot | Method drawPlot |
| drawPlot-method | Method drawPlot |
| genCov | Construct a region of interest coverage plot |
| geneViz | Construct a gene-features plot |
| GenVisR | GenVisR |
| getData | Method getData |
| getData-method | Method getData |
| getDescription | Method getDescription |
| getDescription-method | Method getDescription |
| getGrob | Method getGrob |
| getGrob-method | Method getGrob |
| getHeader | Method getHeader |
| getHeader-method | Method getHeader |
| getMeta | Method getMeta |
| getMeta-method | Method getMeta |
| getMutation | Method getMutation |
| getMutation-method | Method getMutation |
| getPath | Method getPath |
| getPath-method | Method getPath |
| getPosition | Method getPosition |
| getPosition-method | Method getPosition |
| getSample | Method getSample |
| getSample-method | Method getSample |
| getVersion | Method getVersion |
| getVersion-method | Method getVersion |
| GMS | Class GMS |
| GMS-class | Class GMS |
| GMS_v4 | Class GMS_v4 |
| GMS_v4-class | Class GMS_v4 |
| GMS_Virtual-class | Class GMS_Virtual |
| HCC1395_Germline | Germline Calls |
| HCC1395_N | Normal BAM |
| HCC1395_T | Tumor BAM |
| hg19chr | hg19 chromosome boundaries |
| ideoView | Construct an ideogram |
| lohSpec | Plot LOH data |
| lohView | Construct LOH chromosome plot |
| Lolliplot | Class Lolliplot |
| lolliplot | Construct a lolliplot |
| Lolliplot-class | Class Lolliplot |
| lolliplot_AA2sidechain | Convert AA to side chain classification |
| lolliplot_buildMain | Construct Lolliplot |
| LucCNseg | Truncated CN segments |
| MutationAnnotationFormat | Class MutationAnnotationFormat |
| MutationAnnotationFormat-class | Class MutationAnnotationFormat |
| MutationAnnotationFormat_v1.0 | Class MutationAnnotationFormat_v1.0 |
| MutationAnnotationFormat_v1.0-class | Class MutationAnnotationFormat_v1.0 |
| MutationAnnotationFormat_v2.0 | Class MutationAnnotationFormat_v2.0 |
| MutationAnnotationFormat_v2.0-class | Class MutationAnnotationFormat_v2.0 |
| MutationAnnotationFormat_v2.1 | Class MutationAnnotationFormat_v2.1 |
| MutationAnnotationFormat_v2.1-class | Class MutationAnnotationFormat_v2.1 |
| MutationAnnotationFormat_v2.2 | Class MutationAnnotationFormat_v2.2 |
| MutationAnnotationFormat_v2.2-class | Class MutationAnnotationFormat_v2.2 |
| MutationAnnotationFormat_v2.3 | Class MutationAnnotationFormat_v2.3 |
| MutationAnnotationFormat_v2.3-class | Class MutationAnnotationFormat_v2.3 |
| MutationAnnotationFormat_v2.4 | Class MutationAnnotationFormat_v2.4 |
| MutationAnnotationFormat_v2.4-class | Class MutationAnnotationFormat_v2.4 |
| MutationAnnotationFormat_Virtual-class | Class MutationAnnotationFormat_Virtual |
| MutSpectra | Class MutSpectra |
| MutSpectra-class | Class MutSpectra |
| PIK3CA | Subset MAF file for PIK3CA gene |
| Rainfall | Class Rainfall |
| Rainfall-class | Class Rainfall |
| SNPloci | Identity snps |
| TvTi | Construct transition-transversion plot |
| VEP | Class VEP |
| VEP-class | Class VEP |
| VEP_v88 | Class VEP_v88 |
| VEP_v88-class | Class VEP_v88 |
| VEP_Virtual-class | Class VEP_Virtual |
| Waterfall | Class Waterfall |
| waterfall | Construct a waterfall plot |
| Waterfall-class | Class Waterfall |
| writeData | Method writeData |
| writeData,GMS_Virtual | Method writeData |
| writeData,MutationAnnotationFormat_Virtual | Method writeData |
| writeData,VEP_Virtual | Method writeData |
| writeData-method | Method writeData |