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GenVisR (version 1.0.2)
Genomic Visualizations in R
Description
Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.
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Version
1.0.4
1.0.2
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Version
1.0.2
License
GPL-3 + file LICENSE
Maintainer
Zachary Skidmore
Last Published
January 1st, 1970
Functions in GenVisR (1.0.2)
Search functions
SNPloci
Identity snps
compIdent_buildMain
Compare sample identities
cnView
Construct copy-number single sample plot
TvTi
Construct transition-transversion plot
TvTi_convMAF
Convert .maf format to internal format
cnFreq_qual
check input to cnFreq
geneViz_calcGC
Calculate GC content
compIdent
Construct identity snp comparison plot
covBars_buildMain
Construct coverage cohort plot
lohView_buildMain
construct loh plot
genCov_buildCov
build coverage plot
lohSpec_stepCalc
Obtain average loh within each step
cnFreq_buildMain
Construct CN frequency plot
HCC1395_T
Tumor BAM
lolliplot_Codon2AA
Convert Codon to AA
waterfall_MGI2anno
Convert MGI File
genCov_trackViz
Overlay tracks with plots
genCov_assign_ggplotGrob_height
assign ggplotGrob height
geneViz_extrUTR
Extract UTR
multi_selectOut
Choose output
genCov_extr_ggplotGrob_width
extract ggplotGrob width
genCov_assign_ggplotGrob_width
assign ggplotGrob width
lohSpec
Plot LOH data
lohSpec_qual
Check input to lohSpec
multi_align
align CN/LOH plots on x axis
waterfall
Construct a waterfall plot
lolliplot_constructGene
Construct gene information
lolliplot_transcriptID2codingSeq
fetch protein length
waterfall_geneSort
sort waterfall file by gene
lolliplot_qual
Check input to lolliplot
lolliplot_mutationObs
format mutation observations
waterfall_geneRecurCutoff
Mutation Recurrence Cutoff
waterfall_qual
Check input to mutSpec
waterfall_Custom2anno
Convert Custom File
genCov_extr_ggplotGrob_height
extract ggplotGrob height
TvTi_alignPlot
align TvTi plots on y axis
TvTi_calcTransTranvFreq
Calculate Transition/Transversion Frequency
ideoView
Construct an ideogram
genCov
Construct a region of interest coverage plot
TvTi_qual
Check input to TvTi
genCov_alignPlot
align plots on an axis
ideoView_formatCytobands
reformat cytogenetic band data frame
covBars
Construct an overall coverage cohort plot
ideoView_buildMain
build chromosome
brcaMAF
Truncated BRCA MAF file
lolliplot_dodgeCoordX
dodge coordinates
waterfall_buildMain
Plot a mutation heatmap
waterfall_rmvSilent
Silent Mutation Removal
geneViz_extrCDS
Extract CDS
lohSpec_tileWindow
Obtain LOH data
lohView
Construct LOH chromosome plot
genCov_buildTrack
build label for plot
lohSpec_tilePosition
Obtain window information
multi_subsetChr
subset based on chr
waterfall_MAF2anno
Convert MAF File
lolliplot_buildMain
Construct Lolliplot
waterfall_NA2gene
Assign NA samples a gene
waterfall_sampSort
sort samples in an internal waterfall file.
cnView_buildMain
construct CN plot
geneViz_formatCDS
format cds
TvTi_annoTransTranv
Annotate Transitions and Transversions
geneViz_Granges2dataframe
Convert Granges object to dataframe
geneViz_mapCovCoordSpace
Map coverage track regions to transformed space
lohSpec_slidingWindow
Obtain LOH data
lohView_qual
check input to lohView
geneViz_cdsFromTXID
cdsFromTXID
waterfall_buildGenePrevelance
plot mutation recurrence in genes
lolliplot_reduceLolli
Reduce Lolli
GenVisR
GenVisR
TvTi_buildMain
build transitions/transversions
cnFreq
Construct copy-number frequency plot
compIdent_format
Format readcount tables from compIdent
lolliplot_dodgeCoordY
dodge coordinates
TvTi_rmIndel
Remove indels
compIdent_bamRcnt_qual
Count nucleotide reads at SNP locations
waterfall_buildMutBurden_A
plot mutation burden
geneViz_buildGene
build gene plot
geneViz_mergeRegions
Create Region Table
geneViz_mergeTypeRegions
Create Typed Region Table
lohSpec_fileGlob
Grab data for lohSpec
lohSpec_windowPosition
Obtain window information
lolliplot
Construct a lolliplot
waterfall_buildMutBurden_B
plot mutation burden
waterfall_sampAlt
mutation sample subset sample based
HCC1395_N
Normal BAM
cnSpec
Construct copy-number cohort plot
cnSpec_qual
Construct CN cohort plot
geneViz_mergeTypes
Merge Typed Region Tables
lolliplot_DNAconv
Convert DNA character string
multi_cytobandRet
Retrieve cytogenetic bands
waterfall_hierarchyTRV
Hiearchical removal of MAF entries
lohSpec_lohCalc
Calculate loh difference
cnSpec_buildMain
Construct CN cohort plot
geneViz_formatUTR
format UTR
ideoView_qual
Check input to ideoView
lohSpec_tileCalc
Calculate loh difference
multi_chrBound
retrieve and format CN_cohort plot supplemental data
waterfall_align
align plots
waterfall_calcMutFreq
Calculate Synonymous/Nonsynonymous mutation frequency
waterfall_geneAlt
mutation sample cutoff gene based
multi_buildClin
plot clinical information
geneViz
Construct a gene-features plot
TvTi_rmMnuc
Remove multinucleotide codes
cnView_qual
check input to cnView
genCov_qual
Perform quality control on genCov data
compIdent_bamRcnt
Count nucleotide reads at SNP locations
lohSpec_buildMain
Plot LOH data
lolliplot_fetchDomain
fetch protein domains
geneViz_mapCoordSpace
Map regions to transformed space
HCC1395_Germline
Germline Calls
lolliplot_AA2sidechain
Convert AA to side chain classification
cytoGeno
Cytogenetic banding dataset
hg19chr
hg19 chromosome boundaries
covBars_qual
Construct coverage cohort plot
LucCNseg
Truncated CN segments