geneRxCluster: gRx Differential Clustering
Version 1.12.0

Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

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AuthorCharles Berry
Bioconductor views Clustering Genetics Sequencing
Date of publicationNone
MaintainerCharles Berry <ccberry@ucsd.edu>
LicenseGPL (>= 2)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geneRxCluster")

Man pages

critVal.alpha: critical regions
critVal.power: critical regions
critVal.target: critical regions
geneRxCluster: Differential Clustering of Integration Sites
gRxCluster: gRxCluster
gRxCluster-object: gRxCluster object
gRxPlot: gRxPlot
gRxPlotClumps: gRxPlotClumps
gRxSummary: gRxSummary
noprune: noprune
plot.cutpoints: plot.cutpoints
prune.loglik: prune.loglik

Functions

critVal.alpha Man page Source code
critVal.power Man page Source code
critVal.target Man page Source code
gRxCluster Man page Source code Source code
gRxCluster-object Man page
gRxPlot Man page Source code
gRxPlotClumps Man page Source code
gRxSummary Man page Source code
geneRxCluster Man page
geneRxCluster-package Man page
grx_clust_Call Source code
noprune Man page Source code
plot.cutpoints Man page Source code
prune.loglik Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/Rutils.R
R/dot-gRxCluster.R
R/gRxCluster.R
R/gRxPlot.R
R/gRxPlotClumps.R
R/gRxSummary.R
R/geneRxCluster-package.R
R/grx_clust_Call.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/tutorial.R
inst/doc/tutorial.Rnw
inst/doc/tutorial.pdf
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/runit.1.R
man
man/critVal.alpha.Rd
man/critVal.power.Rd
man/critVal.target.Rd
man/gRxCluster-object.Rd
man/gRxCluster.Rd
man/gRxPlot.Rd
man/gRxPlotClumps.Rd
man/gRxSummary.Rd
man/geneRxCluster.Rd
man/noprune.Rd
man/plot.cutpoints.Rd
man/prune.loglik.Rd
src
src/cluster.c
tests
tests/doRunit.R
vignettes
vignettes/tutorial.Rnw
geneRxCluster documentation built on May 20, 2017, 10:12 p.m.