geneRxCluster: gRx Differential Clustering

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.

Author
Charles Berry
Date of publication
None
Maintainer
Charles Berry <ccberry@ucsd.edu>
License
GPL (>= 2)
Version
1.10.0

View on Bioconductor

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

Files in this package

geneRxCluster/DESCRIPTION
geneRxCluster/NAMESPACE
geneRxCluster/R
geneRxCluster/R/Rutils.R
geneRxCluster/R/dot-gRxCluster.R
geneRxCluster/R/gRxCluster.R
geneRxCluster/R/gRxPlot.R
geneRxCluster/R/gRxPlotClumps.R
geneRxCluster/R/gRxSummary.R
geneRxCluster/R/geneRxCluster-package.R
geneRxCluster/R/grx_clust_Call.R
geneRxCluster/build
geneRxCluster/build/vignette.rds
geneRxCluster/inst
geneRxCluster/inst/CITATION
geneRxCluster/inst/doc
geneRxCluster/inst/doc/tutorial.R
geneRxCluster/inst/doc/tutorial.Rnw
geneRxCluster/inst/doc/tutorial.pdf
geneRxCluster/inst/unitTests
geneRxCluster/inst/unitTests/Makefile
geneRxCluster/inst/unitTests/runit.1.R
geneRxCluster/man
geneRxCluster/man/critVal.alpha.Rd
geneRxCluster/man/critVal.power.Rd
geneRxCluster/man/critVal.target.Rd
geneRxCluster/man/gRxCluster-object.Rd
geneRxCluster/man/gRxCluster.Rd
geneRxCluster/man/gRxPlot.Rd
geneRxCluster/man/gRxPlotClumps.Rd
geneRxCluster/man/gRxSummary.Rd
geneRxCluster/man/geneRxCluster.Rd
geneRxCluster/man/noprune.Rd
geneRxCluster/man/plot.cutpoints.Rd
geneRxCluster/man/prune.loglik.Rd
geneRxCluster/src
geneRxCluster/src/cluster.c
geneRxCluster/tests
geneRxCluster/tests/doRunit.R
geneRxCluster/vignettes
geneRxCluster/vignettes/tutorial.Rnw