pint: Pairwise INTegration of functional genomics data

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Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens.

Author
Olli-Pekka Huovilainen <ohuovila@gmail.com> and Leo Lahti <leo.lahti@iki.fi>
Date of publication
None
Maintainer
Olli-Pekka Huovilainen <ohuovila@gmail.com>
License
BSD_2_clause + file LICENSE
Version
1.24.0
URLs

View on Bioconductor

Man pages

ChromosomeModels-class
Class "ChromosomeModels"
fit.byname
Fit dependency model around one gene between two data sets.
geneCopyNum
Gene copy number data in chromosome 17
GeneDependencyModel-class
Class "GeneDependencyModel"
geneExp
Gene expression data in chromosome 17
GenomeModels-class
Class "GenomeModels"
get.neighboring.probes
Get neighboring probes
get.neighs
get.neighs
join.top.regions
Merge the overlapping top chromosomal regions.
order.feature.info
Order the gene information table by chromosomal locations.
pint.data
Forms a data set and pairs samples in two data sets.
plot
Dependency score plotting
screen
Fits dependency models to chromosomal arm, chromosome or the...
summarize.region.parameters
Summarize overlapping models.
window
Form data with a selected window size for the model fitting
z.effect
The model parameters z and W

Files in this package

pint/DESCRIPTION
pint/LICENSE
pint/NAMESPACE
pint/R
pint/R/AllClasses.R
pint/R/AllGenerics.R
pint/R/ChromosomeModels-accessors.R
pint/R/GeneDependencyModel-accessors.R
pint/R/GenomeModels-accessors.R
pint/R/W.effects.R
pint/R/calculate.arm.R
pint/R/calculate.arm.sparse.R
pint/R/calculate.chr.R
pint/R/calculate.chr.sparse.R
pint/R/calculate.genome.R
pint/R/calculate.genome.sparse.R
pint/R/centerData.R
pint/R/firstlib.R
pint/R/fit.cgh.mir.byname.R
pint/R/fit.cgh.mrna.byname.R
pint/R/fixed.window.R
pint/R/imputation.R
pint/R/iterative.window.R
pint/R/pick.chr.arm.R
pint/R/pint.data.R
pint/R/pint.match.R
pint/R/plot-methods.R
pint/R/report.R
pint/R/screen.cgh.mir.R
pint/R/screen.cgh.mrna.R
pint/R/show-methods.R
pint/R/sparse.window.R
pint/R/test.segmented.R
pint/R/z.effects.R
pint/README.md
pint/build
pint/build/vignette.rds
pint/data
pint/data/chromosome17.RData
pint/inst
pint/inst/CITATION
pint/inst/NEWS
pint/inst/doc
pint/inst/doc/depsearch.R
pint/inst/doc/depsearch.Rnw
pint/inst/doc/depsearch.pdf
pint/man
pint/man/ChromosomeModels-class.Rd
pint/man/GeneDependencyModel-class.Rd
pint/man/GenomeModels-class.Rd
pint/man/fit.byname.Rd
pint/man/geneCopyNum.Rd
pint/man/geneExp.Rd
pint/man/get.neighboring.probes.Rd
pint/man/get.neighs.Rd
pint/man/join.top.regions.Rd
pint/man/order.feature.info.Rd
pint/man/pint.data.Rd
pint/man/plot.Rd
pint/man/screen.Rd
pint/man/summarize.region.parameters.Rd
pint/man/window.Rd
pint/man/z.effect.Rd
pint/vignettes
pint/vignettes/cca2.eps
pint/vignettes/cca2.png
pint/vignettes/depsearch-003.eps
pint/vignettes/depsearch-005.eps
pint/vignettes/depsearch.Rnw
pint/vignettes/depsearch.bib