NetRep: Permutation Testing Network Module Preservation Across Datasets

Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.

Install the latest version of this package by entering the following in R:
install.packages("NetRep")
AuthorScott Ritchie [aut, cre]
Date of publication2016-11-16 08:16:22
MaintainerScott Ritchie <sritchie73@gmail.com>
LicenseGPL-2
Version1.0.4

View on CRAN

Functions

as.disk.matrix Man page
as.disk.matrix,ANY-method Man page
as.disk.matrix,disk.matrix-method Man page
as.disk.matrix,matrix-method Man page
as.matrix,disk.matrix-method Man page
attach.disk.matrix Man page
combineAnalyses Man page
common_params Man page
discovery_correlation Man page
discovery_data Man page
discovery_network Man page
disk.matrix Man page
example-data Man page
is.disk.matrix Man page
load.bigMatrix Man page
module_labels Man page
modulePreservation Man page
NetRep Man page
NetRep-data Man page
NetRep-package Man page
networkProperties Man page
nodeOrder Man page
orderModules_param Man page
permutation Man page
permutationTest Man page
permuted Man page
plotContribution Man page
plotCorrelation Man page
plotData Man page
plotDegree Man page
plotModule Man page
plotNetwork Man page
plot_params Man page
plotSummary Man page
plotTopology Man page
requiredPerms Man page
sampleOrder Man page
serialize.table Man page
show,disk.matrix-method Man page
simplify_param Man page
test_correlation Man page
test_data Man page
test_network Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/NetRep.html
inst/doc/NetRep.R
inst/doc/NetRep.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test1-main.R tests/testthat/test2-downstream-analysis.R
src
src/netStats.cpp
src/Makevars
src/netStats.h
src/interrupt.h
src/interrupt.cpp
src/properties.cpp
src/checkFinite.cpp
src/discProps.cpp
src/permutationsNoData.cpp
src/thread-utils.h
src/utils.h
src/utils.cpp
src/permutations.cpp
src/scale.cpp
src/thread-utils.cpp
src/scale.h
src/NetRep_types.h
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
data
data/NetRep.rda
R
R/multi-machine.R R/utils.R R/check-user-input.R R/disk-matrix-class.R R/bigMatrix.R R/orderNodes.R R/modulePreservation.R R/plot-topology.R R/contingency.R R/plot-utils.R R/orderSamples.R R/plot-module.R R/example-data.R R/networkProperties.R R/pperm.R R/RcppExports.R R/NetRep.R R/plot-functions.R R/roxygen-defs.R
vignettes
vignettes/NetRep_files
vignettes/NetRep_files/img
vignettes/NetRep_files/img/preservation.png
vignettes/NetRep_files/img/mod1.png
vignettes/NetRep_files/figure-html
vignettes/NetRep_files/figure-html/dry_run_customised-1.png
vignettes/NetRep_files/figure-html/mean_degree_customised-1.png
vignettes/NetRep_files/figure-html/disk_matrix_dry_run-1.png
vignettes/NetRep_files/figure-html/modules_in_discovery-1.png
vignettes/NetRep_files/figure-html/mean_degree-1.png
vignettes/NetRep_files/figure-html/disk_matrix_plot-1.png
vignettes/NetRep_files/figure-html/correlation_heatmap-1.png
vignettes/NetRep_files/figure-html/modules_in_test-1.png
vignettes/NetRep_files/figure-html/dry_run-1.png
vignettes/NetRep.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/orderModules_param.Rd man/NetRep.Rd man/example-data.Rd man/simplify_param.Rd man/permutationTest.Rd man/nodeOrder.Rd man/requiredPerms.Rd man/sampleOrder.Rd man/plot_params.Rd man/combineAnalyses.Rd man/common_params.Rd man/modulePreservation.Rd man/disk.matrix.Rd man/plotModule.Rd man/networkProperties.Rd man/bigMatrix.Rd man/plotTopology.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.