lpNet: Linear Programming Model for Network Inference
Version 2.8.0

lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.

Browse man pages Browse package API and functions Browse package files

AuthorBettina Knapp, Marta R. A. Matos, Johanna Mazur, Lars Kaderali
Bioconductor views NetworkInference
Date of publicationNone
MaintainerLars Kaderali <lars.kaderali@tu-dresden.de>
LicenseArtistic License 2.0
Version2.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("lpNet")

Man pages

calcActivation: Calculate Activation Matrix
calcPrediction: Calculate Predicted Observation.
calcRangeLambda: Compute Range Of Penalty Parameter Lambda.
CV: Cross-validation
doILP: Do The Network Inference With The Linear Programming...
generateTimeSeriesNetStates: Generate Time Series Network States
getAdja: Get Adjacency Matrix.
getBaseline: Get Baseline Vector.
getEdgeAnnot: Get the annotation of the edges.
getObsMat: Get Observation Matrix.
getSampleAdja: Get The Sample Adjacency.
lpNet-package: Network Inference Of Perturbation Data Using a Linear...
summarizeRepl: Summarize Replicate Measurements

Functions

calcActivation Man page Source code
calcPredictionKfoldCV Man page Source code
calcPredictionKfoldCV_steadyState Source code
calcPredictionKfoldCV_timeSeries Source code
calcPredictionLOOCV Man page Source code
calcPredictionLOOCV_steadyState Source code
calcPredictionLOOCV_timeSeries Source code
calcRangeLambda Man page Source code
calcRangeLambda_steadyState Source code
calcRangeLambda_timeSeries Source code
calculatePredictionValue_Kfold_ts Source code
calculatePredictionValue_LOOCV_ss Source code
calculatePredictionValue_LOOCV_ts Source code
doILP Man page Source code
doILP_steadyState Source code
doILP_timeSeries Source code
generateTimeSeriesNetStates Man page Source code
getAdja Man page Source code
getBaseline Man page Source code
getEdgeAnnot Man page Source code
getNTimePoints Source code
getObsMat Man page Source code
getSampleAdja Man page Source code
getSampleAdjaMAD Man page Source code
kfoldCV Man page Source code
kfoldCV_steadyState Source code
kfoldCV_timeSeries Source code
loocv Man page Source code
loocv_steadyState Source code
loocv_timeSeries Source code
lpNet Man page
lpNet-package Man page
setDeltaValue_KfoldCV_ts Source code
setDeltaValue_LOOCV_ts Source code
setInflow_act Source code
set_per_gene_exp_time_values Source code
set_per_gene_exp_values Source code
set_per_gene_time_values Source code
set_per_gene_values Source code
set_single_values Source code
summarizeRepl Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/calcActivation.R
R/calcPredictionKfoldCV.R
R/calcPredictionLOOCV.R
R/calcRangeLambda.R
R/doILP.R
R/doILP_steadyState.R
R/doILP_timeSeries.R
R/generateTimeSeriesNetStates.r
R/getAdja.R
R/getBaseline.R
R/getEdgeAnnot.R
R/getObsMat.R
R/getSampleAdja.R
R/getSampleAdjaMAD.R
R/kfoldCV.R
R/loocv.R
R/summarizeRepl.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/vignette_lpNet.R
inst/doc/vignette_lpNet.Rnw
inst/doc/vignette_lpNet.pdf
man
man/CV.Rd
man/calcActivation.Rd
man/calcPrediction.Rd
man/calcRangeLambda.Rd
man/doILP.Rd
man/generateTimeSeriesNetStates.Rd
man/getAdja.Rd
man/getBaseline.Rd
man/getEdgeAnnot.Rd
man/getObsMat.Rd
man/getSampleAdja.Rd
man/lpNet-package.Rd
man/summarizeRepl.Rd
tests
tests/runitCalcActivation.R
tests/runitCalcPredictionKfoldCV.R
tests/runitCalcPredictionKfoldCV_timeSeries.R
tests/runitCalcPredictionLOOCV.R
tests/runitCalcPredictionLOOCV_timeSeries.R
tests/runitCalcRangeLambda.R
tests/runitDoILP.R
tests/runitDoILP_timeSeries.R
tests/runitGenerateTimeSeriesNetStates.R
tests/runitGetAdja.R
tests/runitGetBaseline.R
tests/runitGetEdgeAnnot.R
tests/runitGetObsMat.R
tests/runitGetSampleAdja.R
tests/runitGetSampleAdjaMAD.R
tests/runitKfoldCV.R
tests/runitKfoldCV_timeSeries.R
tests/runitLOOCV.R
tests/runitLOOCV_timeSeries.R
vignettes
vignettes/references.bib
vignettes/vignette_lpNet.Rnw
lpNet documentation built on May 20, 2017, 9:38 p.m.