# Genomic Visualizations in R

## Documentation for package ‘GenVisR’ version 1.8.1

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

## Help Pages

B C G H I L M S T W

GenVisR-package | GenVisR

## -- B --

brcaMAF | Truncated BRCA MAF file

## -- C --

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

## -- G --

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_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_Granges2dataframe | Convert Granges object to dataframe
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
GenVisR | GenVisR

## -- H --

HCC1395_Germline | Germline Calls
HCC1395_N | Normal BAM
HCC1395_T | Tumor BAM
hg19chr | hg19 chromosome boundaries

## -- I --

ideoView | Construct an ideogram
ideoView_buildMain | build chromosome
ideoView_formatCytobands | reformat cytogenetic band data frame
ideoView_qual | Check input to ideoView

## -- L --

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_buildMain | Construct Lolliplot
lolliplot_Codon2AA | Convert Codon to AA
lolliplot_constructGene | Construct gene information
lolliplot_DNAconv | Convert DNA character string
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
LucCNseg | Truncated CN segments

## -- M --

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

## -- S --

SNPloci | Identity snps

## -- T --

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_convMaf | Convert .maf format to internal format
TvTi_qual | Check input to TvTi
TvTi_rmIndel | Remove indels
TvTi_rmMnuc | Remove multinucleotide codes

## -- W --

waterfall | Construct a waterfall plot
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_Custom2anno | Convert Custom File
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_MAF2anno | Convert MAF File
waterfall_MGI2anno | Convert MGI File
waterfall_NA2gene | Assign NA samples a gene
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