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SpaCCr (version 0.1.0)

Spatial Convex Clustering

Description

Genomic Region Detection via Spatial Convex Clustering. See for details.

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Version

Install

install.packages('SpaCCr')

Monthly Downloads

18

Version

0.1.0

License

GPL-3

Maintainer

John Nagorski

Last Published

November 23rd, 2016

Functions in SpaCCr (0.1.0)

MethyRegionPlot

Plots methylation data by Genomic Coordinates for a given chromosomal region with cluster means overlayed for each subject.
PlotCV

A function for plotting cross validation errors
ThreshV

Threshold differences
SpaCC_Path

Solve Spatial Convex Clustering problem for path of regularization parameters
SpaCC

Base function for computing SpaCC solution for single regularization value.
SpaCC_CV

Perform Cross Validation to select gamma/sparsity level
SpaCC_Methy

Performs Spatial Convex Clustering for methylation data
hello

Hello, World!
methy

A subset of methylation data for 50 subjects
GetGammaCV

Get optimal cross validated gamma values by various rules
GetParBlocks

Function to compute blocks for parallization; should not be called directly
SpaCC_Missing

Solve Spatial Convex Clustering problem for missing data
SpaCC_Path_Parallel

Solve Spatial Convex Clustering problem for path of regularization parameters in parallel
CNVPlotSeriesMeans

Plot subjects' copy number data with cluster means overlayed for a single chromosome
GetClusters

Compute Clusters from fusions