Package 'CARNIVAL' reference manual

Title:	A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Description:	An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.
Authors:	Enio Gjerga [aut] , Panuwat Trairatphisan [aut], Anika Liu [ctb], Alberto Valdeolivas [ctb], Nikolas Peschke [ctb], Aurelien Dugourd [ctb], Attila Gabor [cre], Olga Ivanova [aut]
Maintainer:	Attila Gabor <[email protected]>
License:	GPL-3
Version:	2.17.0
Built:	2024-10-30 04:29:05 UTC
Source:	https://github.com/bioc/CARNIVAL

Checks if provided option names are valid.

Description

Checks if provided option names are valid.

Usage

checkOptionsValidity(solver = getSupportedSolvers()$lpSolve, ...)
checkOptionsValidity(solver = getSupportedSolvers()$lpSolve, ...)

Arguments

`solver`	one of the solvers available from getSupportedSolvers().
`...`	any possible options from the solver's list

Value

TRUE/FALSE depending on the status of the checks

Examples

checkOptionsValidity(solver="lpSolve")
checkOptionsValidity(solver="lpSolve")

Sets default CARNIVAL options for cbc.

Description

Sets default CARNIVAL options for cbc.

Usage

defaultCbcSolveCarnivalOptions(...)
defaultCbcSolveCarnivalOptions(...)

Arguments

...

any possible options from the solver's list

Value

default CbB solver options as a list.

Examples

#defaultCbcSolveCarnivalOptions()
#defaultCbcSolveCarnivalOptions()

Sets default CARNIVAL options for cplex.

Description

Sets default CARNIVAL options for cplex.

Usage

defaultCplexCarnivalOptions(...)
defaultCplexCarnivalOptions(...)

Arguments

...

any possible options from the solver's list

Value

default CPLEX solver options as a list.

Examples

defaultCplexCarnivalOptions()
defaultCplexCarnivalOptions()

Sets default options from cplex documentation.

Description

Sets default options from cplex documentation.

Usage

defaultCplexSpecificOptions(...)
defaultCplexSpecificOptions(...)

Arguments

...

any possible options from the solver's list

Value

default CPLEX solver options as a list.

Examples

defaultCplexSpecificOptions()
defaultCplexSpecificOptions()

Sets default CARNIVAL options for lpSolve.

Description

Sets default CARNIVAL options for lpSolve.

Usage

defaultLpSolveCarnivalOptions(...)
defaultLpSolveCarnivalOptions(...)

Arguments

...

any possible options from the solver's list

Value

default lpSolve solver options as a list.

Examples

defaultLpSolveCarnivalOptions()
defaultLpSolveCarnivalOptions()

`generateLpFileCarnival`

Description

generateLpFileCarnival

Usage

generateLpFileCarnival(
  perturbations = NULL,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)
generateLpFileCarnival(
  perturbations = NULL,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

`perturbations`	(optional, if inverse CARNIVAL flavour is used further) vector of targets of perturbations.
`measurements`	vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores)
`priorKnowledgeNetwork`	data frame of the prior knowledge network
`weights`	(optional) vector of the additional weights: e.g. PROGENy pathway scores or measured protein activities.
`carnivalOptions`	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultCplexCarnivalOptions, defaultCbcCarnivalOptions.

Details

Prepares the input data for the run: tranforms data into lp file and .Rdata file. These files can be reused to run CARNIVAL without preprocessing step using runCarnivalFromLp(..)

Value

paths to .lp file and .RData file that can be used for runFromLpCarnival()

Examples

load(file = system.file("toy_perturbations_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                        package="CARNIVAL"))

## lpSolve
#res1 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
#                             measurements = toy_measurements_ex1,
#                             priorKnowledgeNetwork = toy_network_ex1,
#                             carnivalOptions = defaultLpSolveCarnivalOptions())

#res1["lpFile"] ##path to generated lp file
#res1["parsedDataFile"] ##path to data file used during generation

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                               measurements = toy_measurements_ex1,
##                               priorKnowledgeNetwork = toy_network_ex1,
##                               carnivalOptions = defaultCbcCarnivalOptions())
##
## res2["lpFile"] ##path to generated lp file
## res2["parsedDataFile"] ##path to data file used during generation
##
## cplex
## res3 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                              measurements = toy_measurements_ex1,
##                              priorKnowledgeNetwork = toy_network_ex1,
##                              carnivalOptions = defaultCplexCarnivalOptions())
##
## res3["lpFile"] ##path to generated lp file
## res3["parsedDataFile"] ##path to data file used during generation
load(file = system.file("toy_perturbations_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                        package="CARNIVAL"))

## lpSolve
#res1 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
#                             measurements = toy_measurements_ex1,
#                             priorKnowledgeNetwork = toy_network_ex1,
#                             carnivalOptions = defaultLpSolveCarnivalOptions())

#res1["lpFile"] ##path to generated lp file
#res1["parsedDataFile"] ##path to data file used during generation

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                               measurements = toy_measurements_ex1,
##                               priorKnowledgeNetwork = toy_network_ex1,
##                               carnivalOptions = defaultCbcCarnivalOptions())
##
## res2["lpFile"] ##path to generated lp file
## res2["parsedDataFile"] ##path to data file used during generation
##
## cplex
## res3 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                              measurements = toy_measurements_ex1,
##                              priorKnowledgeNetwork = toy_network_ex1,
##                              carnivalOptions = defaultCplexCarnivalOptions())
##
## res3["lpFile"] ##path to generated lp file
## res3["parsedDataFile"] ##path to data file used during generation

Returns the list of options needed/supported for each solver.

Description

Returns the list of options needed/supported for each solver.

Usage

getOptionsList(solver = "", onlyRequired = FALSE)
getOptionsList(solver = "", onlyRequired = FALSE)

Arguments

`solver`	one of the solvers available from getSupportedSolvers()
`onlyRequired`	logic, set to TRUE if you want to obtain only required options for the run

Value

list of options, solver-dependent

Returns the list of supported solvers.

Description

Returns the list of supported solvers.

Usage

getSupportedSolvers()
getSupportedSolvers()

Value

list of currently supported solvers.

Checks validity of all inputs of CARNIVAL

Description

Checks validity of all inputs of CARNIVAL

Usage

isInputValidCarnival(
  perturbations = NULL,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)
isInputValidCarnival(
  perturbations = NULL,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

`perturbations`	(optional, if inverse CARNIVAL flavour is used further) vector of targets of perturbations.
`measurements`	vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores)
`priorKnowledgeNetwork`	data frame of the prior knowledge network
`weights`	(optional) vector of the additional weights: e.g. PROGENy pathway scores or measured protein activities.
`carnivalOptions`	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultCplexCarnivalOptions, defaultCbcCarnivalOptions.

Value

TRUE if everything passed the checks.

Examples

load(file = system.file("toy_perturbations_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                        package="CARNIVAL"))

## lpSolve
#isInputValidCarnival(perturbations = toy_perturbations_ex1,
#                    measurements = toy_measurements_ex1,
#                    priorKnowledgeNetwork = toy_network_ex1,
#                    carnivalOptions = defaultLpSolveCarnivalOptions())
load(file = system.file("toy_perturbations_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                        package="CARNIVAL"))

## lpSolve
#isInputValidCarnival(perturbations = toy_perturbations_ex1,
#                    measurements = toy_measurements_ex1,
#                    priorKnowledgeNetwork = toy_network_ex1,
#                    carnivalOptions = defaultLpSolveCarnivalOptions())

Parses the cplex log file and reads some basic information.

Description

Parses the cplex log file and reads some basic information.

Usage

parseCplexLog(log)
parseCplexLog(log)

Arguments

log

path of log file resulted from a carnival run OR the content of this file read by read_lines.

Value

list variable with following fields: - 'convergence' a table that contains information on the convergence of CPLEX - 'n_solutions' number of solutions found - 'objective' objective function value - 'termination_reason': reason of termination

Author(s)

Attila Gabor, 2021

`runCARNIVAL`

Description

runCARNIVAL

Usage

runCARNIVAL(
  inputObj = NULL,
  measObj = measObj,
  netObj = netObj,
  weightObj = NULL,
  solverPath = NULL,
  solver = c("lpSolve", "cplex", "cbc", "gurobi"),
  timelimit = 3600,
  mipGAP = 0.05,
  poolrelGAP = 1e-04,
  limitPop = 500,
  poolCap = 100,
  poolIntensity = 4,
  poolReplace = 2,
  alphaWeight = 1,
  betaWeight = 0.2,
  threads = 0,
  cleanTmpFiles = TRUE,
  keepLPFiles = TRUE,
  clonelog = -1,
  dir_name = getwd()
)
runCARNIVAL(
  inputObj = NULL,
  measObj = measObj,
  netObj = netObj,
  weightObj = NULL,
  solverPath = NULL,
  solver = c("lpSolve", "cplex", "cbc", "gurobi"),
  timelimit = 3600,
  mipGAP = 0.05,
  poolrelGAP = 1e-04,
  limitPop = 500,
  poolCap = 100,
  poolIntensity = 4,
  poolReplace = 2,
  alphaWeight = 1,
  betaWeight = 0.2,
  threads = 0,
  cleanTmpFiles = TRUE,
  keepLPFiles = TRUE,
  clonelog = -1,
  dir_name = getwd()
)

Arguments

`inputObj`	Data frame of the list for target of perturbation - optional or default set to NULL to run invCARNIVAL when inputs are not known.
`measObj`	Data frame of the measurement file (i.e. DoRothEA normalised enrichment scores) - always required.
`netObj`	Data frame of the prior knowledge network - always required.
`weightObj`	Data frame of the additional weight (i.e. PROGENy pathway score or measured protein activities) - optional or default set as NULL to run CARNIVAL without weights.
`solverPath`	Path to executable cbc/cplex file - default set to NULL, in which case the solver from lpSolve package is used.
`solver`	Solver to use: lpSolve/cplex/cbc (Default set to lpSolve).
`timelimit`	CPLEX/Cbc parameter: Time limit of CPLEX optimisation in seconds (default set to 3600).
`mipGAP`	CPLEX parameter: the absolute tolerance on the gap between the best integer objective and the objective of the best node remaining. When this difference falls below the value of this parameter, the linear integer optimization is stopped (default set to 0.05)
`poolrelGAP`	CPLEX/Cbc parameter: Allowed relative gap of accepted solution comparing within the pool of accepted solution (default: 0.0001)
`limitPop`	CPLEX parameter: Allowed number of solutions to be generated (default: 500)
`poolCap`	CPLEX parameter: Allowed number of solution to be kept in the pool of solution (default: 100)
`poolIntensity`	CPLEX parameter: Intensity of solution searching (0,1,2,3,4 - default: 4)
`poolReplace`	CPLEX parameter: Replacement strategy of solutions in the pool (0,1,2 - default: 2 = most diversified solutions)
`alphaWeight`	Objective function: weight for mismatch penalty (default: 1 - will only be applied once measurement file only contains discrete values)
`betaWeight`	Objective function: weight for node penalty (default: 0.2)
`threads`	CPLEX/CBC parameter: Number of threads to use default: 0 for maximum number possible threads on system
`cleanTmpFiles`	logic (default-TRUE), specifying if the tmp files made by solvers should be cleaned after run.
`keepLPFiles`	logic (default=TRUE), specifying if the LP file should be kept.
`clonelog`	determines if CPLEX clones the log files in case of multi-threaded optimization, default: -1, (no cloning)
`dir_name`	Specify directory name to store results. by default set to NULL

Details

Run CARNIVAL pipeline using to the user-provided list of inputs or run CARNIVAL built-in examples. The function is from v1.2 of CARNIVAL and is left for backward compatibility.

Value

The function will return a list of results containing:

1. weightedSIF: A table with 4 columns containing the combined network solutions from CARNIVAL. It contains the Source of the interaction (Node1), Sign of the interaction (Sign), the Target of the interaction (Node2) and the weight of the interaction (Weight) which shows how often an interaction appears across all solutions.

2. nodesAttributes: A table with 6 columns containing information about infered protein activity states and attributes. It contains the Protein IDs (Node); how often this node has taken an activity of 0, 1 and -1 across the solutions (ZeroAct, UpAct, DownAct); the average activities across solutions (AvgAct); and the node attribute (measured, target, inferred).

3. sifAll: A list of separate network solutions.

4. attributesAll: A list of separate inferred node activities in each solution.

5. diagnostics: reports the convergence of optimization and reason of the termination. Only for CPLEX solver.

Author(s)

Enio Gjerga, 2020 [email protected]

Examples

load(file = system.file("toy_perturbations_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runCARNIVAL(inputObj = toy_perturbations_ex1,
#                    measObj = toy_measurements_ex1,
#                    netObj = toy_network_ex1,
#                    solver = 'lpSolve')

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runCARNIVAL(inputObj = toy_perturbations_ex1,
##                    measObj = toy_measurements_ex1,
##                    netObj = toy_network_ex1,
##                    solver = 'cbc')
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runCARNIVAL(inputObj = toy_perturbations_ex1,
##                    measObj = toy_measurements_ex1,
##                    netObj = toy_network_ex1,
##                    solver = 'cplex')
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

load(file = system.file("toy_perturbations_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runCARNIVAL(inputObj = toy_perturbations_ex1,
#                    measObj = toy_measurements_ex1,
#                    netObj = toy_network_ex1,
#                    solver = 'lpSolve')

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runCARNIVAL(inputObj = toy_perturbations_ex1,
##                    measObj = toy_measurements_ex1,
##                    netObj = toy_network_ex1,
##                    solver = 'cbc')
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runCARNIVAL(inputObj = toy_perturbations_ex1,
##                    measObj = toy_measurements_ex1,
##                    netObj = toy_network_ex1,
##                    solver = 'cplex')
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

`runCarnivalFromLp`

Description

runCarnivalFromLp

Usage

runFromLpCarnival(
  lpFile = "",
  parsedDataFile = "",
  carnivalOptions = defaultLpSolveCarnivalOptions()
)
runFromLpCarnival(
  lpFile = "",
  parsedDataFile = "",
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

`lpFile`	full path to .lp file
`parsedDataFile`	full path to preprocessed .RData file
`carnivalOptions`	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultLpSolveCarnivalOptions, defaultCbcCarnivalOptions.

Details

Runs CARNIVAL pipeline with preparsed data - lp file and Rdata file containing variables for ILP formulation.

Value

The function will return a list of results containing: 1. weightedSIF: A table with 4 columns containing the combined network solutions from CARNIVAL. It contains the Source of the interaction (Node1), Sign of the interaction (Sign), the Target of the interaction (Node2) and the weight of the interaction (Weight) which shows how often an interaction appears across all solutions.

3. sifAll: A list of separate network solutions.

4. attributesAll: A list of separate inferred node activities in each solution.

5. diagnostics: reports the convergence of optimization and reason of the termination. Only for CPLEX solver.

Author(s)

Enio Gjerga, Olga Ivanova 2020-2021 [email protected]

Examples

lpFilePath = system.file("toy_lp_file_ex1.lp",
                         package="CARNIVAL")

parsedDataFilePath = system.file("toy_parsed_data_ex1.RData",
                                package="CARNIVAL")

## lpSolve
#res1 = runFromLpCarnival(lpFile = lpFilePath,
#                         parsedDataFile = parsedDataFilePath,
#                         carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runFromLpCarnival(lpFile = lpFilePath,
##                          parsedDataFile = parsedDataFilePath,
##                          carnivalOptions = defaultLpCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runFromLpCarnival(lpFile = lpFilePath,
##                          parsedDataFile = parsedDataFilePath,
##                          carnivalOptions = defaultLpCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

lpFilePath = system.file("toy_lp_file_ex1.lp",
                         package="CARNIVAL")

parsedDataFilePath = system.file("toy_parsed_data_ex1.RData",
                                package="CARNIVAL")

## lpSolve
#res1 = runFromLpCarnival(lpFile = lpFilePath,
#                         parsedDataFile = parsedDataFilePath,
#                         carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runFromLpCarnival(lpFile = lpFilePath,
##                          parsedDataFile = parsedDataFilePath,
##                          carnivalOptions = defaultLpCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runFromLpCarnival(lpFile = lpFilePath,
##                          parsedDataFile = parsedDataFilePath,
##                          carnivalOptions = defaultLpCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

`runInverseCarnival`

Description

runInverseCarnival

Usage

runInverseCarnival(
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)
runInverseCarnival(
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

`measurements`	vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores)
`priorKnowledgeNetwork`	data frame of the prior knowledge network
`weights`	(optional) vector of the additional weights: e.g. PROGENy pathway score or measured protein activities.
`carnivalOptions`	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultLpSolveCarnivalOptions, defaultCbcCarnivalOptions.

Details

TODO Replace with correct description

Value

The function will return a list of results containing:

3. sifAll: A list of separate network solutions.

4. attributesAll: A list of separate inferred node activities in each solution.

5. diagnostics: reports the convergence of optimization and reason of the termination. Only for CPLEX solver.

Author(s)

Enio Gjerga, Olga Ivanova 2020-2021 [email protected]

Examples

load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runInverseCarnival(measurements = toy_measurements_ex1,
#                          priorKnowledgeNetwork = toy_network_ex1,
#                          carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runInverseCarnival(measurements = toy_measurements_ex1,
##                           priorKnowledgeNetwork = toy_network_ex1,
##                           carnivalOptions = defaultCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runVanillaCarnival(measurements = toy_measurements_ex1,
##                           priorKnowledgeNetwork = toy_network_ex1,
##                           carnivalOptions = defaultCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runInverseCarnival(measurements = toy_measurements_ex1,
#                          priorKnowledgeNetwork = toy_network_ex1,
#                          carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runInverseCarnival(measurements = toy_measurements_ex1,
##                           priorKnowledgeNetwork = toy_network_ex1,
##                           carnivalOptions = defaultCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runVanillaCarnival(measurements = toy_measurements_ex1,
##                           priorKnowledgeNetwork = toy_network_ex1,
##                           carnivalOptions = defaultCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

`runVanillaCarnival`

Description

runVanillaCarnival

Usage

runVanillaCarnival(
  perturbations,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)
runVanillaCarnival(
  perturbations,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

`perturbations`	vector of targets of perturbations.
`measurements`	vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores)
`priorKnowledgeNetwork`	data frame of the prior knowledge network
`weights`	(optional) vector of the additional weights: e.g. PROGENy pathway score or measured protein activities.
`carnivalOptions`	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultLpSolveCarnivalOptions, defaultCbcCarnivalOptions.

Details

Runs full CARNIVAL pipeline, vanilla(classic) flavour.

Value

3. sifAll: A list of separate network solutions.

4. attributesAll: A list of separate inferred node activities in each solution.

5. diagnostics: reports the convergence of optimization and reason of the termination. Only for CPLEX solver.

Author(s)

Enio Gjerga, Olga Ivanova 2020-2021 [email protected]

Examples

load(file = system.file("toy_perturbations_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
#                          measurements = toy_measurements_ex1,
#                          priorKnowledgeNetwork = toy_network_ex1,
#                          carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
##                               measurements = toy_measurements_ex1,
##                               priorKnowledgeNetwork = toy_network_ex1,
##                               carnivalOptions = defaultCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
##                              measurements = toy_measurements_ex1,
##                              priorKnowledgeNetwork = toy_network_ex1,
##                              carnivalOptions = defaultCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

load(file = system.file("toy_perturbations_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                       package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                       package="CARNIVAL"))

## lpSolve
#res1 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
#                          measurements = toy_measurements_ex1,
#                          priorKnowledgeNetwork = toy_network_ex1,
#                          carnivalOptions = defaultLpSolveCarnivalOptions())

#res1$weightedSIF ##see @return
#res1$nodesAttributes ## see @return
#res1$sifAll ## see @return
#res1$attributesAll ## see @return

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
##                               measurements = toy_measurements_ex1,
##                               priorKnowledgeNetwork = toy_network_ex1,
##                               carnivalOptions = defaultCbcCarnivalOptions())
##
## res2$weightedSIF ##see @return
## res2$nodesAttributes ## see @return
## res2$sifAll ## see @return
## res2$attributesAll ## see @return
##
## cplex
## res3 = runVanillaCarnival(perturbations = toy_perturbations_ex1,
##                              measurements = toy_measurements_ex1,
##                              priorKnowledgeNetwork = toy_network_ex1,
##                              carnivalOptions = defaultCplexCarnivalOptions())
##
## res3$weightedSIF ##see @return
## res3$nodesAttributes ## see @return
## res3$sifAll ## see @return
## res3$attributesAll ## see @return

Sets CARNIVAL options for the solver.

Description

Sets CARNIVAL options for the solver.

Usage

setCarnivalOptions(solver = getSupportedSolvers()$lpSolve, ...)
setCarnivalOptions(solver = getSupportedSolvers()$lpSolve, ...)

Arguments

`solver`	one of the solvers available from getSupportedSolvers().
`...`	any possible options from the solver's list

Value

carnival options as list.

Examples

setCarnivalOptions(solver="lpSolve")
setCarnivalOptions(solver="lpSolve")

Suggests cbc specific options.

Description

Suggests cbc specific options.

Usage

suggestedCbcSpecificOptions(...)
suggestedCbcSpecificOptions(...)

Arguments

...

any possible options from the solver's list

Value

additional CbC solver options as a list.

Examples

suggestedCbcSpecificOptions()
suggestedCbcSpecificOptions()

Suggests cplex specific options.s

Description

Suggests cplex specific options.s

Usage

suggestedCplexSpecificOptions(...)
suggestedCplexSpecificOptions(...)

Arguments

...

any possible options from the solver's list

Value

additional CPLEX solver options as a list.

Examples

suggestedCplexSpecificOptions()
suggestedCplexSpecificOptions()

writeCplexCommandFileFromJson

Description

writeCplexCommandFileFromJson

Usage

writeCplexCommandFileFromJson(
  carnivalOptions,
  jsonFileName = "parameters/cplex_parameters_cmd_file.json"
)
writeCplexCommandFileFromJson(
  carnivalOptions,
  jsonFileName = "parameters/cplex_parameters_cmd_file.json"
)

Arguments

`carnivalOptions`	list of options for the CPLEX solver
`jsonFileName`	name to JSONfile containing the solver parameters

Value

list of params

Package 'CARNIVAL'

Help Index

Checks if provided option names are valid.

Description

Usage

Arguments

Value

Examples

Sets default CARNIVAL options for cbc.

Description

Usage

Arguments

Value

Examples

Sets default CARNIVAL options for cplex.

Description

Usage

Arguments

Value

Examples

Sets default options from cplex documentation.

Description

Usage

Arguments

Value

Examples

Sets default CARNIVAL options for lpSolve.

Description

Usage

Arguments

Value

Examples

generateLpFileCarnival

Description

Usage

Arguments

Details

Value

Examples

Returns the list of options needed/supported for each solver.

Description

Usage

Arguments

Value

Returns the list of supported solvers.

Description

Usage

Value

Checks validity of all inputs of CARNIVAL

Description

Usage

Arguments

Value

Examples

Parses the cplex log file and reads some basic information.

Description

Usage

Arguments

Value

Author(s)

runCARNIVAL

Description

Usage

Arguments

Details

Value

Author(s)

Examples

runCarnivalFromLp

Description

Usage

Arguments

Details

Value

Author(s)

Examples

runInverseCarnival

Description

Usage

Arguments

`generateLpFileCarnival`

`runCARNIVAL`

`runCarnivalFromLp`

`runInverseCarnival`

`runVanillaCarnival`