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                Method drawPlot
genCov                  Construct a region of interest coverage plot
geneViz                 Construct a gene-features plot
GenVisR                 GenVisR
getData                 Method getData
getDescription          Method getDescription
getGrob                 Method getGrob
getHeader               Method getHeader
getMeta                 Method getMeta
getMutation             Method getMutation
getPath                 Method getPath
getPosition             Method getPosition
getSample               Method getSample
getVersion              Method getVersion
GMS_v4-class            Class GMS_v4
GMS_Virtual-class       Class GMS_Virtual
GMS-class               Class GMS
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_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
MutationAnnotationFormat-class
                        Class MutationAnnotationFormat
MutSpectra-class        Class MutSpectra
PIK3CA                  Subset MAF file for PIK3CA gene
Rainfall-class          Class Rainfall
SNPloci                 Identity snps
TvTi                    Construct transition-transversion plot
VEP_v88-class           Class VEP_v88
VEP_Virtual-class       Class VEP_Virtual
VEP-class               Class VEP
waterfall               Construct a oncoprint
Waterfall-class         Class Waterfall
writeData               Method writeData
