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.

Author
Scott Ritchie [aut, cre]
Date of publication
2016-11-16 08:16:22
Maintainer
Scott Ritchie <sritchie73@gmail.com>
License
GPL-2
Version
1.0.4

View on CRAN

Man pages

bigMatrix
Load a 'bigMatrix' (deprecated)
combineAnalyses
Combine results of multiple permutation procedures
common_params
Template parameters
disk.matrix
The 'disk.matrix' class
example-data
Example data
modulePreservation
Replication and preservation of network modules across...
NetRep
Fast permutation procedure for testing network module...
networkProperties
Calculate the topological properties for a network module
nodeOrder
Order nodes in descending order of _weighted degree_ and...
orderModules_param
Template parameters
permutationTest
Permutation test P-values for module preservation statistics
plotModule
Plot the topology of a network module
plot_params
Template parameters
plotTopology
Plot a topological feature of network module
requiredPerms
How many permutations do I need to test at my desired...
sampleOrder
Order samples within a network.
simplify_param
Template parameters

Files in this package

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