SANTA: Spatial Analysis of Network Associations

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This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).

Author
Alex J. Cornish and Florian Markowetz
Date of publication
None
Maintainer
Alex J. Cornish <a.cornish12@imperial.ac.uk>
License
GPL (>= 2)
Version
2.12.0

View on Bioconductor

Man pages

BinGraph
Compute a distance bin matrix from a distance matrix
Compactness
Measure the strength of association using compactness scores
CreateGrid
Generate a grid-like network
DistGraph
Compute the vertex pair distance matrix for a graph
GraphDiffusion
Compute diffusion kernel-based distance matrix
GraphMFPT
Compute mean first-passage time-based distance matrix
Knet
Measure the strength of association between a phenotype and a...
Knode
Rank vertices by their strength of association with...
plot.Knet
Plot the results of the 'Knet' function
SANTA.data
Pre-processed dataset for the SANTA vignette
SpreadHits
Spread hits across a network in clusters

Files in this package

SANTA/DESCRIPTION
SANTA/NAMESPACE
SANTA/NEWS
SANTA/R
SANTA/R/AsiGraph.R
SANTA/R/BinGraph.R
SANTA/R/CheckAttributes.R
SANTA/R/Compactness.R
SANTA/R/ComputeWeightsInBins.R
SANTA/R/CreateGrid.R
SANTA/R/DistGraph.R
SANTA/R/GraphDiffusion.R
SANTA/R/GraphMFPT.R
SANTA/R/Knet.R
SANTA/R/Knode.R
SANTA/R/Shuffle.R
SANTA/R/SpreadHits.R
SANTA/R/plot.Knet.R
SANTA/build
SANTA/build/vignette.rds
SANTA/data
SANTA/data/datalist
SANTA/data/edgelist.humannet.RData
SANTA/data/edgelist.intact.RData
SANTA/data/g.bandyopadhyay.treated.RData
SANTA/data/g.bandyopadhyay.untreated.RData
SANTA/data/g.costanzo.cor.RData
SANTA/data/g.costanzo.raw.RData
SANTA/data/g.srivas.high.RData
SANTA/data/g.srivas.untreated.RData
SANTA/data/go.entrez.RData
SANTA/data/rnai.cheung.RData
SANTA/inst
SANTA/inst/CITATION
SANTA/inst/doc
SANTA/inst/doc/SANTA-vignette.R
SANTA/inst/doc/SANTA-vignette.Rmd
SANTA/inst/doc/SANTA-vignette.html
SANTA/inst/unitTests
SANTA/inst/unitTests/test_AsiGraph.R
SANTA/inst/unitTests/test_BinGraph.R
SANTA/inst/unitTests/test_CheckAttributes.R
SANTA/inst/unitTests/test_Compactness.R
SANTA/inst/unitTests/test_ComputeWeightsInBins.R
SANTA/inst/unitTests/test_CreateGrid.R
SANTA/inst/unitTests/test_DistGraph.R
SANTA/inst/unitTests/test_GraphDiffusion.R
SANTA/inst/unitTests/test_GraphMFPT.R
SANTA/inst/unitTests/test_Knet.R
SANTA/inst/unitTests/test_Knode.R
SANTA/inst/unitTests/test_Shuffle.R
SANTA/inst/unitTests/test_SpreadHits.R
SANTA/man
SANTA/man/BinGraph.Rd
SANTA/man/Compactness.Rd
SANTA/man/CreateGrid.Rd
SANTA/man/DistGraph.Rd
SANTA/man/GraphDiffusion.Rd
SANTA/man/GraphMFPT.Rd
SANTA/man/Knet.Rd
SANTA/man/Knode.Rd
SANTA/man/SANTA.data.Rd
SANTA/man/SpreadHits.Rd
SANTA/man/plot.Knet.Rd
SANTA/src
SANTA/src/computenetK_fewzeros.c
SANTA/src/computenetK_manyzeros.c
SANTA/src/computenodeAUK.c
SANTA/src/computeweights.c
SANTA/tests
SANTA/tests/runTests.R
SANTA/vignettes
SANTA/vignettes/SANTA-vignette.Rmd
SANTA/vignettes/fig_bionet_simulation.jpg
SANTA/vignettes/fig_case_3_association.jpg
SANTA/vignettes/fig_dna_1.jpg
SANTA/vignettes/fig_dna_2.jpg
SANTA/vignettes/refs.bib