SpaCCr: Spatial Convex Clustering

Genomic Region Detection via Spatial Convex Clustering. See <https://arxiv.org/abs/1611.04696> for details.

Author
John Nagorski
Date of publication
2016-11-23 09:38:35
Maintainer
John Nagorski<jn13@rice.edu>
License
GPL-3
Version
0.1.0

View on CRAN

Man pages

CNVPlotSeriesMeans
Plot subjects' copy number data with cluster means overlayed...
GetClusters
Compute Clusters from fusions
GetGammaCV
Get optimal cross validated gamma values by various rules
GetParBlocks
Function to compute blocks for parallization; should not be...
hello
Hello, World!
methy
A subset of methylation data for 50 subjects
MethyRegionPlot
Plots methylation data by Genomic Coordinates for a given...
PlotCV
A function for plotting cross validation errors
SpaCC
Base function for computing SpaCC solution for single...
SpaCC_CV
Perform Cross Validation to select gamma/sparsity level
SpaCC_Methy
Performs Spatial Convex Clustering for methylation data
SpaCC_Missing
Solve Spatial Convex Clustering problem for missing data
SpaCC_Path
Solve Spatial Convex Clustering problem for path of...
SpaCC_Path_Parallel
Solve Spatial Convex Clustering problem for path of...
ThreshV
Threshold differences

Files in this package

SpaCCr
SpaCCr/tests
SpaCCr/tests/testthat.R
SpaCCr/tests/testthat
SpaCCr/tests/testthat/test_basicrun.R
SpaCCr/src
SpaCCr/src/Makevars
SpaCCr/src/SpaCC.cpp
SpaCCr/src/RcppExports.cpp
SpaCCr/NAMESPACE
SpaCCr/data
SpaCCr/data/methy.rda
SpaCCr/R
SpaCCr/R/data.R
SpaCCr/R/RcppExports.R
SpaCCr/R/SpaCCRFunctions.R
SpaCCr/R/stub.R
SpaCCr/R/hello.R
SpaCCr/MD5
SpaCCr/DESCRIPTION
SpaCCr/man
SpaCCr/man/SpaCC_Path_Parallel.Rd
SpaCCr/man/GetClusters.Rd
SpaCCr/man/SpaCC.Rd
SpaCCr/man/PlotCV.Rd
SpaCCr/man/SpaCC_Path.Rd
SpaCCr/man/SpaCC_Missing.Rd
SpaCCr/man/SpaCC_Methy.Rd
SpaCCr/man/SpaCC_CV.Rd
SpaCCr/man/GetParBlocks.Rd
SpaCCr/man/GetGammaCV.Rd
SpaCCr/man/ThreshV.Rd
SpaCCr/man/methy.Rd
SpaCCr/man/CNVPlotSeriesMeans.Rd
SpaCCr/man/MethyRegionPlot.Rd
SpaCCr/man/hello.Rd