Man pages for griffithlab/GenVisR
Genomic Visualizations in R
| brcaMAF | Truncated BRCA MAF file |
| 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-methods | Method drawPlot |
| genCov | Construct a region of interest coverage plot |
| geneViz | Construct a gene-features plot |
| GenVisR | GenVisR |
| getData-methods | Method getData |
| getDescription-methods | Method getDescription |
| getGrob-methods | Method getGrob |
| getHeader-methods | Method getHeader |
| getMeta-methods | Method getMeta |
| getMutation-methods | Method getMutation |
| getPath-methods | Method getPath |
| getPosition-methods | Method getPosition |
| getSample-methods | Method getSample |
| getVersion-methods | Method getVersion |
| GMS-class | Class GMS |
| 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 | Construct a lolliplot |
| Lolliplot-class | Class Lolliplot |
| LucCNseg | Truncated CN segments |
| MutationAnnotationFormat-class | Class MutationAnnotationFormat |
| MutationAnnotationFormat_v1.0-class | Class MutationAnnotationFormat_v1.0 |
| MutationAnnotationFormat_v2.0-class | Class MutationAnnotationFormat_v2.0 |
| MutationAnnotationFormat_v2.1-class | Class MutationAnnotationFormat_v2.1 |
| MutationAnnotationFormat_v2.2-class | Class MutationAnnotationFormat_v2.2 |
| MutationAnnotationFormat_v2.3-class | Class MutationAnnotationFormat_v2.3 |
| MutationAnnotationFormat_v2.4-class | Class MutationAnnotationFormat_v2.4 |
| MutationAnnotationFormat_Virtual-class | Class MutationAnnotationFormat_Virtual |
| MutSpectra-class | Class MutSpectra |
| PIK3CA | Subset MAF file for PIK3CA gene |
| Rainfall-class | Class Rainfall |
| SNPloci | Identity snps |
| TvTi | Construct transition-transversion plot |
| VEP-class | Class VEP |
| VEP_v88-class | Class VEP_v88 |
| VEP_Virtual-class | Class VEP_Virtual |
| waterfall | Construct a oncoprint |
| Waterfall-class | Class Waterfall |
| writeData-methods | Method writeData |
