# Genomic Visualizations in R

## Documentation for package ‘GenVisR’ version 1.22.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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