SANTA: Spatial Analysis of Network Associations
Version 2.14.0

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).

Browse man pages Browse package API and functions Browse package files

AuthorAlex J. Cornish and Florian Markowetz
Bioconductor views Clustering Network NetworkEnrichment
Date of publicationNone
MaintainerAlex J. Cornish <a.cornish12@imperial.ac.uk>
LicenseGPL (>= 2)
Version2.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SANTA")

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

Functions

AsiGraph Source code
BinGraph Man page Source code
CheckAttributes Source code
Compactness Man page Source code
ComputeWeightsInBins Source code
CreateGrid Man page Source code
Diffusionfct Source code
DistGraph Man page Source code
GraphDiffusion Man page Source code
GraphMFPT Man page Source code
Knet Man page Source code
Knode Man page Source code
MFPTfct Source code
Shuffle Source code
SpreadHits Man page Source code
edgelist.humannet Man page
edgelist.intact Man page
g.bandyopadhyay.treated Man page
g.bandyopadhyay.untreated Man page
g.costanzo.cor Man page
g.costanzo.raw Man page
g.srivas.high Man page
g.srivas.untreated Man page
go.entrez Man page
plot.Knet Man page Source code
rnai.cheung Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AsiGraph.R
R/BinGraph.R
R/CheckAttributes.R
R/Compactness.R
R/ComputeWeightsInBins.R
R/CreateGrid.R
R/DistGraph.R
R/GraphDiffusion.R
R/GraphMFPT.R
R/Knet.R
R/Knode.R
R/Shuffle.R
R/SpreadHits.R
R/plot.Knet.R
build
build/vignette.rds
data
data/datalist
data/edgelist.humannet.RData
data/edgelist.intact.RData
data/g.bandyopadhyay.treated.RData
data/g.bandyopadhyay.untreated.RData
data/g.costanzo.cor.RData
data/g.costanzo.raw.RData
data/g.srivas.high.RData
data/g.srivas.untreated.RData
data/go.entrez.RData
data/rnai.cheung.RData
inst
inst/CITATION
inst/doc
inst/doc/SANTA-vignette.R
inst/doc/SANTA-vignette.Rmd
inst/doc/SANTA-vignette.html
inst/unitTests
inst/unitTests/test_AsiGraph.R
inst/unitTests/test_BinGraph.R
inst/unitTests/test_CheckAttributes.R
inst/unitTests/test_Compactness.R
inst/unitTests/test_ComputeWeightsInBins.R
inst/unitTests/test_CreateGrid.R
inst/unitTests/test_DistGraph.R
inst/unitTests/test_GraphDiffusion.R
inst/unitTests/test_GraphMFPT.R
inst/unitTests/test_Knet.R
inst/unitTests/test_Knode.R
inst/unitTests/test_Shuffle.R
inst/unitTests/test_SpreadHits.R
man
man/BinGraph.Rd
man/Compactness.Rd
man/CreateGrid.Rd
man/DistGraph.Rd
man/GraphDiffusion.Rd
man/GraphMFPT.Rd
man/Knet.Rd
man/Knode.Rd
man/SANTA.data.Rd
man/SpreadHits.Rd
man/plot.Knet.Rd
src
src/computenetK_fewzeros.c
src/computenetK_manyzeros.c
src/computenodeAUK.c
src/computeweights.c
tests
tests/runTests.R
vignettes
vignettes/SANTA-vignette.Rmd
vignettes/fig_bionet_simulation.jpg
vignettes/fig_case_3_association.jpg
vignettes/fig_dna_1.jpg
vignettes/fig_dna_2.jpg
vignettes/refs.bib
SANTA documentation built on May 20, 2017, 10:01 p.m.