Man pages for GenVisR
Genomic Visualizations in R

brcaMAFTruncated BRCA MAF file
cnFreqConstruct copy-number frequency plot
cnFreq_buildMainConstruct CN frequency plot
cnFreq_qualcheck input to cnFreq
cnSpecConstruct copy-number cohort plot
cnSpec_buildMainConstruct CN cohort plot
cnSpec_qualConstruct CN cohort plot
cnViewConstruct copy-number single sample plot
cnView_buildMainconstruct CN plot
cnView_qualcheck input to cnView
compIdentConstruct identity snp comparison plot
compIdent_bamRcntCount nucleotide reads at SNP locations
compIdent_bamRcnt_qualCount nucleotide reads at SNP locations
compIdent_buildMainCompare sample identities
compIdent_formatFormat readcount tables from compIdent
covBarsConstruct an overall coverage cohort plot
covBars_buildMainConstruct coverage cohort plot
covBars_qualConstruct coverage cohort plot
cytoGenoCytogenetic banding dataset
genCovConstruct a region of interest coverage plot
genCov_alignPlotalign plots on an axis
genCov_assign_ggplotGrob_heightassign ggplotGrob height
genCov_assign_ggplotGrob_widthassign ggplotGrob width
genCov_buildCovbuild coverage plot
genCov_buildTrackbuild label for plot
genCov_extr_ggplotGrob_heightextract ggplotGrob height
genCov_extr_ggplotGrob_widthextract ggplotGrob width
genCov_qualPerform quality control on genCov data
genCov_trackVizOverlay tracks with plots
geneVizConstruct a gene-features plot
geneViz_buildGenebuild gene plot
geneViz_calcGCCalculate GC content
geneViz_cdsFromTXIDcdsFromTXID
geneViz_extrCDSExtract CDS
geneViz_extrUTRExtract UTR
geneViz_formatCDSformat cds
geneViz_formatUTRformat UTR
geneViz_Granges2dataframeConvert Granges object to dataframe
geneViz_mapCoordSpaceMap regions to transformed space
geneViz_mapCovCoordSpaceMap coverage track regions to transformed space
geneViz_mergeRegionsCreate Region Table
geneViz_mergeTypeRegionsCreate Typed Region Table
geneViz_mergeTypesMerge Typed Region Tables
GenVisRGenVisR
HCC1395_GermlineGermline Calls
HCC1395_NNormal BAM
HCC1395_TTumor BAM
hg19chrhg19 chromosome boundaries
ideoViewConstruct an ideogram
ideoView_buildMainbuild chromosome
ideoView_formatCytobandsreformat cytogenetic band data frame
ideoView_qualCheck input to ideoView
lohSpecPlot LOH data
lohSpec_buildMainPlot LOH data
lohSpec_fileGlobGrab data for lohSpec
lohSpec_lohCalcCalculate loh difference
lohSpec_qualCheck input to lohSpec
lohSpec_slidingWindowObtain LOH data
lohSpec_stepCalcObtain average loh within each step
lohSpec_tileCalcCalculate loh difference
lohSpec_tilePositionObtain window information
lohSpec_tileWindowObtain LOH data
lohSpec_windowPositionObtain window information
lohViewConstruct LOH chromosome plot
lohView_buildMainconstruct loh plot
lohView_qualcheck input to lohView
lolliplotConstruct a lolliplot
lolliplot_AA2sidechainConvert AA to side chain classification
lolliplot_buildMainConstruct Lolliplot
lolliplot_Codon2AAConvert Codon to AA
lolliplot_constructGeneConstruct gene information
lolliplot_DNAconvConvert DNA character string
lolliplot_dodgeCoordXdodge coordinates
lolliplot_dodgeCoordYdodge coordinates
lolliplot_fetchDomainfetch protein domains
lolliplot_mutationObsformat mutation observations
lolliplot_qualCheck input to lolliplot
lolliplot_reduceLolliReduce Lolli
lolliplot_transcriptID2codingSeqfetch protein length
LucCNsegTruncated CN segments
multi_alignalign CN/LOH plots on x axis
multi_buildClinplot clinical information
multi_chrBoundretrieve and format CN_cohort plot supplemental data
multi_cytobandRetRetrieve cytogenetic bands
multi_selectOutChoose output
multi_subsetChrsubset based on chr
SNPlociIdentity snps
TvTiConstruct transition-transversion plot
TvTi_alignPlotalign TvTi plots on y axis
TvTi_annoTransTranvAnnotate Transitions and Transversions
TvTi_buildMainbuild transitions/transversions
TvTi_calcTransTranvFreqCalculate Transition/Transversion Frequency
TvTi_convMAFConvert .maf format to internal format
TvTi_qualCheck input to TvTi
TvTi_rmIndelRemove indels
TvTi_rmMnucRemove multinucleotide codes
waterfallConstruct a waterfall plot
waterfall_alignalign plots
waterfall_buildGenePrevelanceplot mutation recurrence in genes
waterfall_buildMainPlot a mutation heatmap
waterfall_buildMutBurden_Aplot mutation burden
waterfall_buildMutBurden_Bplot mutation burden
waterfall_build_proportionsBuild mutational profile plot
waterfall_calcMutFreqCalculate Synonymous/Nonsynonymous mutation frequency
waterfall_Custom2annoConvert Custom File
waterfall_geneAltmutation sample cutoff gene based
waterfall_geneRecurCutoffMutation Recurrence Cutoff
waterfall_geneSortsort waterfall file by gene
waterfall_hierarchyTRVHiearchical removal of MAF entries
waterfall_MAF2annoConvert MAF File
waterfall_MGI2annoConvert MGI File
waterfall_NA2geneAssign NA samples a gene
waterfall_palette_nameswaterfall_palette_names
waterfall_qualCheck input to mutSpec
waterfall_rmvSilentSilent Mutation Removal
waterfall_sampAltmutation sample subset sample based
waterfall_sampSortsort samples in an internal waterfall file.
waterfall_select_paletteHelper function to select a colour palette
GenVisR documentation built on Nov. 17, 2017, 10:41 a.m.