RSVSim: RSVSim: an R/Bioconductor package for the simulation of structural variations
Version 1.16.0

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

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AuthorChristoph Bartenhagen
Bioconductor views Sequencing
Date of publicationNone
MaintainerChristoph Bartenhagen <christoph.bartenhagen@uni-muenster.de>
LicenseLGPL-3
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RSVSim")

Man pages

compareSVs: Compare the simulation with a set of SVs
estimateSVSizes: Draw random structural variation sizes from a beta...
segmentalDuplications: Segmental duplications
simulateSV: Structural Variant Simulation
weightsMechanisms: Weights for SV formation mechanisms
weightsRepeats: Weights for repeat region bias

Functions

addBreakpointMutations Source code
adjustPositions Source code
compareSV Man page Source code
compareSV,character,character-method Man page
compareSV,character,data.frame-method Man page
compareSV,data.frame,data.frame-method Man page
drawPos Source code
drawPos_trans Source code
estimateSVSizes Man page
estimateSVSizes,numeric,missing,ANY,ANY,character-method Man page
estimateSVSizes,numeric,missing,ANY,ANY,missing-method Man page
estimateSVSizes,numeric,numeric,ANY,ANY,missing-method Man page
execDeletion Source code
execInsertion Source code
execInversion Source code
execTandemDuplication Source code
execTranslocation Source code
getBpSeq Source code
getDummyDataframe Source code
getHG19 Source code
getOverlap Source code
getSVSizes Source code
loadFromBSGenome_TandemRepeats Source code
loadFromUCSC_RepeatMasks Source code
loadFromUCSC_SegDups Source code
readRepeatMaskerOutput Source code
segDups Man page
simInsertionPositions Source code
simPositions Source code
simTranslocationPositions Source code
simulateSV Man page
simulateSV,ANY Man page
simulateSV,ANY-method Man page
subtractIntervals Source code
testSVSim Source code
validateInput Source code
weightsMechanisms Man page
weightsRepeats Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/Main.R
R/Misc.R
R/Rearrangement.R
R/Simulation.R
build
build/vignette.rds
data
data/segmentalDuplications.RData
data/weightsMechanisms.RData
data/weightsRepeats.RData
inst
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
man
man/compareSVs.Rd
man/estimateSVSizes.Rd
man/segmentalDuplications.Rd
man/simulateSV.Rd
man/weightsMechanisms.Rd
man/weightsRepeats.Rd
vignettes
vignettes/vignette.Rnw
RSVSim documentation built on May 20, 2017, 10:40 p.m.