GenVisR                 GenVisR
HCC1395_Germline        Germline Calls
HCC1395_N               Normal BAM
HCC1395_T               Tumor BAM
LucCNseg                Truncated CN segments
SNPloci                 Identity snps
TvTi                    Construct transition-transversion plot
TvTi_alignPlot          align TvTi plots on y axis
TvTi_annoTransTranv     Annotate Transitions and Transversions
TvTi_buildMain          build transitions/transversions
TvTi_calcTransTranvFreq
                        Calculate Transition/Transversion Frequency
TvTi_convMAF            Convert .maf format to internal format
TvTi_qual               Check input to TvTi
TvTi_rmIndel            Remove indels
TvTi_rmMnuc             Remove multinucleotide codes
brcaMAF                 Truncated BRCA MAF file
cnFreq                  Construct copy-number frequency plot
cnFreq_buildMain        Construct CN frequency plot
cnFreq_qual             check input to cnFreq
cnSpec                  Construct copy-number cohort plot
cnSpec_buildMain        Construct CN cohort plot
cnSpec_qual             Construct CN cohort plot
cnView                  Construct copy-number single sample plot
cnView_buildMain        construct CN plot
cnView_qual             check input to cnView
compIdent               Construct identity snp comparison plot
compIdent_bamRcnt       Count nucleotide reads at SNP locations
compIdent_bamRcnt_qual
                        Count nucleotide reads at SNP locations
compIdent_buildMain     Compare sample identities
compIdent_format        Format readcount tables from compIdent
covBars                 Construct an overall coverage cohort plot
covBars_buildMain       Construct coverage cohort plot
covBars_qual            Construct coverage cohort plot
cytoGeno                Cytogenetic banding dataset
genCov                  Construct a region of interest coverage plot
genCov_alignPlot        align plots on an axis
genCov_assign_ggplotGrob_height
                        assign ggplotGrob height
genCov_assign_ggplotGrob_width
                        assign ggplotGrob width
genCov_buildCov         build coverage plot
genCov_buildTrack       build label for plot
genCov_extr_ggplotGrob_height
                        extract ggplotGrob height
genCov_extr_ggplotGrob_width
                        extract ggplotGrob width
genCov_qual             Perform quality control on genCov data
genCov_trackViz         Overlay tracks with plots
geneViz                 Construct a gene-features plot
geneViz_Granges2dataframe
                        Convert Granges object to dataframe
geneViz_buildGene       build gene plot
geneViz_calcGC          Calculate GC content
geneViz_cdsFromTXID     cdsFromTXID
geneViz_extrCDS         Extract CDS
geneViz_extrUTR         Extract UTR
geneViz_formatCDS       format cds
geneViz_formatUTR       format UTR
geneViz_mapCoordSpace   Map regions to transformed space
geneViz_mapCovCoordSpace
                        Map coverage track regions to transformed space
geneViz_mergeRegions    Create Region Table
geneViz_mergeTypeRegions
                        Create Typed Region Table
geneViz_mergeTypes      Merge Typed Region Tables
hg19chr                 hg19 chromosome boundaries
ideoView                Construct an ideogram
ideoView_buildMain      build chromosome
ideoView_formatCytobands
                        reformat cytogenetic band data frame
ideoView_qual           Check input to ideoView
lohSpec                 Plot LOH data
lohSpec_buildMain       Plot LOH data
lohSpec_fileGlob        Grab data for lohSpec
lohSpec_lohCalc         Calculate loh difference
lohSpec_qual            Check input to lohSpec
lohSpec_slidingWindow   Obtain LOH data
lohSpec_stepCalc        Obtain average loh within each step
lohSpec_tileCalc        Calculate loh difference
lohSpec_tilePosition    Obtain window information
lohSpec_tileWindow      Obtain LOH data
lohSpec_windowPosition
                        Obtain window information
lohView                 Construct LOH chromosome plot
lohView_buildMain       construct loh plot
lohView_qual            check input to lohView
lolliplot               Construct a lolliplot
lolliplot_AA2sidechain
                        Convert AA to side chain classification
lolliplot_Codon2AA      Convert Codon to AA
lolliplot_DNAconv       Convert DNA character string
lolliplot_buildMain     Construct Lolliplot
lolliplot_constructGene
                        Construct gene information
lolliplot_dodgeCoordX   dodge coordinates
lolliplot_dodgeCoordY   dodge coordinates
lolliplot_fetchDomain   fetch protein domains
lolliplot_mutationObs   format mutation observations
lolliplot_qual          Check input to lolliplot
lolliplot_reduceLolli   Reduce Lolli
lolliplot_transcriptID2codingSeq
                        fetch protein length
multi_align             align CN/LOH plots on x axis
multi_buildClin         plot clinical information
multi_chrBound          retrieve and format CN_cohort plot supplemental
                        data
multi_cytobandRet       Retrieve cytogenetic bands
multi_selectOut         Choose output
multi_subsetChr         subset based on chr
waterfall               Construct a waterfall plot
waterfall_Custom2anno   Convert Custom File
waterfall_MAF2anno      Convert MAF File
waterfall_MGI2anno      Convert MGI File
waterfall_NA2gene       Assign NA samples a gene
waterfall_align         align plots
waterfall_buildGenePrevelance
                        plot mutation recurrence in genes
waterfall_buildMain     Plot a mutation heatmap
waterfall_buildMutBurden_A
                        plot mutation burden
waterfall_buildMutBurden_B
                        plot mutation burden
waterfall_build_proportions
                        Build mutational profile plot
waterfall_calcMutFreq   Calculate Synonymous/Nonsynonymous mutation
                        frequency
waterfall_geneAlt       mutation sample cutoff gene based
waterfall_geneRecurCutoff
                        Mutation Recurrence Cutoff
waterfall_geneSort      sort waterfall file by gene
waterfall_hierarchyTRV
                        Hiearchical removal of MAF entries
waterfall_palette_names
                        waterfall_palette_names
waterfall_qual          Check input to mutSpec
waterfall_rmvSilent     Silent Mutation Removal
waterfall_sampAlt       mutation sample subset sample based
waterfall_sampSort      sort samples in an internal waterfall file.
waterfall_select_palette
                        Helper function to select a colour palette
