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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

Version

1.0.2

License

GPL-3 + file LICENSE

Maintainer

Zachary Skidmore

Last Published

February 15th, 2017

Functions in GenVisR (1.0.2)

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