R: Function to recover Auto Regressive TIme-VArying interactions...
ARTIVAsubnet
R Documentation
Function to recover Auto Regressive TIme-VArying interactions between a gene of
interest (referred to as "target gene") and a set of genes which may explain the expression of the target gene.
Description
This function generates Reversible Jump MCMC (RJ-MCMC)
sampling for approximating the posterior distribution of a time varying
regulatory network, under the Auto Regressive TIme VArying (ARTIVA) model
(for a detailed description of the algorithm, see Lebre et al.
BMC Systems Biology, 2010).
Starting from time-course gene expression measurements for a gene of
interest (referred to as "target gene") and a set of genes (referred to
as "parent genes") which may explain the expression of the target gene, the
ARTIVA procedure identifies temporal segments for which a set of
interactions occur between the "parent genes" and the "target gene".
The time points that delimit the different temporal segments are referred to as changepoints (CP).
If the measurements time delay is short enough so that the expression of
the target gene depends more likely on the expression of the parent
genes at some previous time points, then the time delay for the
interactions can be chosen with argument dyn. In that case the set of
parent genes may contain the target gene (auto-regulation). Otherwise,
contemporaneous measurements of the parent genes are used to explain the
expression of the target gene and argument dyn is set to 0. In the
latter case, the target gene must be kept out of the set of possible
parent genes.
The ARTIVA algorithm uses a combination of efficient and robust methods:
(1) dynamical Bayesian networks (DBN) to model directed regulatory
interactions between the parent genes and the analyzed target gene
(2) RJ-MCMC sampling for inferring - simultaneously - (a) the time
position (changepoints) at which the regulatory interactions between
the parent genes and the target gene changes and (b) the regulatory
network topologies (interactions between parent and target genes)
associated with the temporal segments delimited by the changepoints.
If available, repeated measurements can be used, the design of
experiments must be specified with argument dataDescription.
A vector with the temporal gene expression measurements for the target gene (i.e. the gene whose regulation factors are looked for).
parentData
A matrix (or a vector if only 1 parent gene) with the temporal gene
expression measurements for the proposed parent genes (i.e. potential
regulation factors). Parent genes are shown in row and expression values
in column. For computational reasons, we advise not to test
simultaneously more than 10 parent genes.
targetName
Name of the target gene (optional, default: targetName="Target").
parentNames
A vector with the names for parent gene(s) (optional, default:
parentNames=NULL).
dataDescription
(Required only when the gene expression measurements contain repeated
values for the same time points). A vector indicating the ordering of
the time measurements in the data. For example
dataDescription=rep(1:n, each=2), if there are two measurements for
each time point AND the repetitions for each time point are next to
each other. Note that temporal gene expression measurements have to be
organized identically in arguments targetData and
parentData (optional, default: dataDescription=NULL).
saveEstimations
Boolean, if TRUE all estimated posterior distributions are saved
as text files either in a new sub folder named "ARTIVA_Results" created
by default in the current folder or in a folder specified with argument
outputPath (see below) (optional, default:
saveEstimations=TRUE).
saveIterations
Boolean, if TRUE the configuration for all iterations is saved as
text files either in a new sub folder named "ARTIVA_Results" created
by default in the current folder or in a folder specified with argument
outputPath (see below) (optional, default:
saveIterations=FALSE).
savePictures
Boolean, if TRUE all estimated posterior distributions and
networks are plotted in a pdf file either in a new sub folder named
"ARTIVA_Results" created by default in the current folder or in a
folder specified with argument outputPath (see below)
(optional, default: savePictures=TRUE).
outputPath
File path to a folder in which the output results have to be saved,
either a complete path or the name of a folder to be created in the
current directory (optional, default: outputPath=NULL).
dyn
Time delay to be considered in the auto-regressive process, between the
temporal expression measurements of the analyzed target gene and the
ones of the parent genes (optional, default: dyn=1).
segMinLength
Minimal length (number of time points) to define a temporal
segment. Must be - strictly - greater than 1 if there is no
repeated measurements for each time point in arguments
targetData and parentData (optional, default: segMinLength=2).
maxCP
Maximal number of CPs to be considered by the ARTIVA inference
procedure. Note that for a temporal course with n time points
the maximal number of CPs is (n-1-dyn) (see before for a
description of argument dyn). For long temporal courses (more
than 20 time points), we advise - for computational reasons - to limit
the maximal number of CP to 15 (optional, default: maxCP=NULL,
if maxCP=NULL then the maximal number of CPs is set to
maxCP=min(round((n-1-dyn)/segMinLength)-1, 15) where n is the
number of time points).
maxPred
Maximal number of simultaneous incoming edges for each segment of the
regulatory network estimated for the target gene (default:
maxPred=NULL, if maxPred=NULL then the maximal number of
incoming edges is set to
maxPred=min(dim(parentData)[1],15))
nbCPinit
Number of CPs to be considered at the algorithm initialization
(optional, default: nbCPinit=NULL, if nbCPinit=NULL then the
initial number of CPs is randomly set to a value between 0 and maxCP/2.).
CPinit
A vector with the initial positions for potential CPs.
(optional, default: CPinit = NULL, if CPinit = NULL
then the initial vector is chosen randomly according to priors, with
nbCPinit changepoints (see previous argument nbCPinit) ).
niter
Number of iterations to be performed in the RJ-MCMC sampling
(optional, default: niter = 50000).
burn_in
Number of initial iterations that are discarded for the estimation of
the model distribution (posterior distribution). The
ARTIVAsubnet function is a RJ-MCMC algorithm which, at
each iteration, randomly samples a new configuration of the
time-varying regulatory network from probability distributions based
on constructing a Markov chain that has the network model distribution
as its equilibrium distribution (The equilibrium distribution is
obtained when the Markov Chain converges, which requires a large
number of iterations).
Typically, initial iterations are notconfident because the Markov Chain
has not stabilized. The burn-in samples allow to not consider these
initial iterations in the final analysis (optional, default:
burn_in=NULL, if burn_in=NULL then the first 25% of the
iterations is left for burn_in).
PSRFactor
Boolean, if TRUE the RJ-MCMC procedure is stopped when the Potential
Scale Ratio Factor or PSRF (which is a usual convergence criterion) is
below a specified threshold (see documentation for argument
PSRF_thres below) or when the maximal number of iterations is
reached (see documentation for argument niter previously) (optional, default: PSRFactor=FALSE).
For more details about the PSRF criterion, see Gelman and Rubin (1992).
PSRF_thres
(Only when PSRFactor=TRUE) RJ-MCMC stopping threshold: the
RJ-MCMC procedure is stopped when the Potential Scale Ratio Factor
(PSRF) is below this threshold (see documentation for argument
PSRFactor previously). Values of the PSRF below 1.1 are usually
taken as indication of sufficient convergence (optional, default:
PSRF_threshold=1.05).
segmentAnalysis
Boolean, if TRUE the posterior distribution for the edges in each
temporal segment delimited by the estimated changepoints (CPs) is
computed. (The estimated CPs are the k CPs with maximal posterior
probability, where k is the number of CPs having the maximal
porsterior probability (such that each temporal segment is larger than
segMinLength) (see documentation below for output values
CPpostDist, nbSegs, CPposition. If segmentAnalysis=FALSE only the posterior distributions of the CPs number and CPs positions are computed (optional, default: segmentAnalysis=TRUE).
edgesThreshold
Probability threshold for the selection of the edges of the time-varying
regulatory network when segmentAnalysis=TRUE
(optional, default: edgesThreshold=0.5).
layout
Name of the function determining the placement of the vertices for
drawing a graph, possible values among others: "random", "circle", "sphere",
"fruchterman.reingold", "kamada.kawai","spring",
"reingold.tilford", "fruchterman.reingold.grid",
see package igraph0 for more details (default:
layout="fruchterman.reingold").
cCP
Maximal probability to propose the birth (resp. death) of a changepoint
(CP) during the RJ-MCMC iterations (optional, default: cCP=0.5).
cEdges
Maximal probability - when a move update of the network topology is
chosen - to propose ecah edge move (birth or death of an edge) within a
temporal segment (optional, default: cEdges=0.5).
alphaCP
Hyperparameter for sampling the number k of CPs. k follows
a Gamma distribution: Gamma(alphaCP, betaCP (see below)) (optional,
default: alphaCP=1). Note that function
choosePriors can be used to choose alphaCP (or betaCP) according to the desired dimension penalisation.
betaCP
Hyperparameter for sampling the number k of CPs. k follows
a Gamma distribution: Gamma(alphaCP (see before), betaCP)
(optional, default: betaCP=0.5). Note that function
choosePriors can be used to choose betaCP (or
alphaCP) according to the desired dimension penalisation.
alphaEdges
Hyperparameter for sampling the number l of regulatory
interactions between the target gene and the parent genes. l
follows a Gamma distribution: rgamma(1, shape=alphaEdges, rate=betaEdges) (see betaEdges below), (default:
alphaEdges=1). Function choosePriors can be used to
choose alphaEdges (or betaEdges) according to
the desired dimension penalisation.
betaEdges
Hyperparameter for sampling the number l of regulatory
interactions between the target gene and the parent genes. l
follows a Gamma distribution: rgamma(1,shape=alphaEdges, rate=betaEdges) (see alphaEdges upper) (optional, default:
betaEdges=0.5). Function choosePriors can be used
to choose betaEdges (or alphaEdges) according to the desired
dimension penalisation.
v0
Hyperparameter for sampling the noise variance (denoted by Sig2)
in the auto-regressive model defining the regulatory time vrarying network. The prior
distribution of the noise variance is an Inverse Gamma distribution with
shape parameter v0/2 and scale parameter gamma0/2: rinvgamma(1,shape=v0/2,scale = gamma0), (optional, default: v0=1).
gamma0
Hyperparameter for sampling the noise variance (denoted by Sig2) in the ARTIVA package) in the auto-regressive
model defining the regulatory time vrarying network. The prior
distribution of the noise variance is an Inverse Gamma distribution with
shape parameter v0/2 and scale parameter gamma0/2: rinvgamma(1,shape=v0/2, scale = gamma0), (optional, default: gamma0=0.1).
alphad2
Hyperparameter for sampling a parameter that represents the expected
signal-to-noise ratio (denoted by delta2 in the ARTIVA
package). It is sampled according to an Inverse Gamma distribution:
rinvgamma(1, shape=alphad2,scale=betad2), (optional, default:
alphad2=2).
betad2
Hyperparameter for sampling a parameter that represents the expected
signal-to-noise ratio (denoted by delta2 in the ARTIVA
package). It is sampled according to an Inverse Gamma distribution:
rinvgamma(1, shape=alphad2,scale=betad2), (optional, default: betad2=0.2).
silent
Boolean, if TRUE messages are printed along the ARTIVA procedure (optional, default: silent=FALSE).
Value
Samples
Results obtained at each iteration of the RJ-MCMC procedure. Samples is list composed of the following elements:
1) Samples$CP: a matrix with in row the different iterations
performed with the ARTIVAsubnet function and in column the identified positions for CPs (if the parameter dyn=1, first CP=2 and final CP=n+1, with n the number of time points);
2) Samples$Edges: a matrix with in row the different ARTIVA iterations and in column the
number of regulatory interactions identified in each temporal phases (-1 values are default
values, when no temporal phase exist);
3) Samples$coeff: a matrix with in row the different ARTIVA iterations and in column the
coefficient values corresponding to the identified regulatory interactions.
4) Samples$variance: a matrix with in row the different ARTIVA iterations and in column the
variance values modelling data noise for each identified temporal phase.
Counters
Results obtained at each iteration of the RJ-MCMC procedure. Counters is list composed of the following elements:
1) Counters$CPMovesCount: Number of modifications PROPOSED during ARTIVA iterations in term
of CPs (i.e. birth of a new CP, death of an existing CP, move of an existing
CP or upate of regulatory models in each temporal phases).
2) Counters$CPMovesAcceptationPrct: Percentage of modifications ACCEPTED during ARTIVA iterations in term
of CPs (i.e. birth of a new CP, death of an existing CP, move of an existing
CP or upate of regulatory models in each temporal phases).
3) Counters$EdgesMoveCount: Number of modifications PROPOSED during
ARTIVA iterations in term of regulatory models (i.e. birth of a new edge between parent and target genes, death of an
existing edge or update of the regression coefficient for existing edges).
4) Counters$EdgesMovesAcceptationPrct: Percentage of modifications ACCEPTED
during ARTIVA iterations in term of regulatory models (i.e. birth of a
new edge between parent and target genes, death of an existing edge or update of the regression coefficient for existing edges).
5) Counters$iterations: Total number of iterations generated by the
ARTIVA procedure.
6) Counters$rcvgce: (only if PSRFactor=TRUE) Number of iterations before
the stopping criterion is reached, i.e. before the PSRF factor is below
the threshold specified with argument PSRF_thres. The returned value
is NULL if the stopping criterion is not reached.
CPpostDist
A list of 2 tables :
1) CPpostDist$CPnumberPostDist: A table containing the approximated distribution for the number of CPs.
2)CPpostDist$CPpositionPostDist: A table containing the approximated distribution for the position of the CPs.
nbSegs
An integer equal to the number of temporal segments with the largest value observed in the posterior distribution (see previously CPnumberPostDist).
SegmentPostDist
(only when parameter
segmentAnalysis=TRUE) A list of tables:
1) SegmentPostDist$CPpos: A table containing the most
significant CP positions that delimit nbSegs temporal segments,
according to CPpostDist$CPnumber, CPpostDist$CPposition and
segMinLength (if parameter dyn=1, first CP is 2
and final CP is n+1, where n is the number of time
points).
2) SegmentPostDist$edgesPostDist: A table containing the approximate posterior distribution for the incoming edges (regulatory
interaction between parent and target genes) for each temporal segment
delimited by the CP given in SegmentPostDist$CPpos (see previously). Each raw corresponds to a segment, ordered by time.
3) SegmentPostDist$edgesCoeff A table containing the estimated
coefficients for the incoming edges (regulatory interaction between
parent and target genes) for each temporal segment delimited by the CP given in SegmentPostDist$CPpos (see previously). Each raw corresponds to a segment, ordered by time.
network
A table containing the information to plot (see function
traceNetworks) the network estimated with the ARTIVAsubnet procedure.
GLOBvar
A list of parameters used in the ARTIVAsubnet procedure
HYPERvar
A list of hyperparameters used in the ARTIVAsubnet procedure
OUTvar
A list of output parameters used in the ARTIVAsubnet procedure.
targetData
targetData vector given as input of the ARTIVAsubnet procedure.
parentData
parentData matrix given as input of the ARTIVAsubnet procedure.
Author(s)
S. Lebre and G. Lelandais
References
S. Lebre, J. Becq, F. Devaux, M. P. H. Stumpf, G. Lelandais (2010)
Statistical inference of the time-varying structure of gene-regulation
networks
BMC Systems Biology, 4:130.
Gelman, A. and D. Rubin (1992)
Inference from iterative simulation using multiple sequences.
Statistical science 7 (4), 457-472.
# Load the ARTIVA R package
library(ARTIVA)
# Load the dataset with simulated gene expression profiles
data(simulatedProfiles)
# Name of the target gene to be analyzed with ARTIVA
targetGene = 1
# Names of the parent genes (typically transcription factors)
parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")
###
# ARTIVA analysis searching for potential interactions between the target
# genes and a predefined list of parent genes.
###
# Note that the number of iterations in the RJ-MCMC sampling is reduced
# to in this example to 'niter=20000' (in order obtain a quick overview
# of the ARTIVAnet fonction, but it should be increased (e.g. up to
# 50000) for a better parameter estimation.
# Without saving the output pictures "savePictures=FALSE"
## Not run:
ARTIVAtest = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
parentData = simulatedProfiles[parentGenes,],
targetName = targetGene,
parentNames = parentGenes,
segMinLength = 2,
edgesThreshold = 0.5,
niter = 20000,
savePictures=FALSE)
# By default, the output results (pictures and estimation values) are
# saved in a folder named "ARTIVAsubnet" created in the current directory
ARTIVAtest = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
parentData = simulatedProfiles[parentGenes,],
targetName = targetGene,
parentNames = parentGenes,
segMinLength = 2,
edgesThreshold = 0.5,
niter = 20000)
# In order to save the results in a specific folder, for example a
# folder entitled "ARTIVA-test" in the current directory:
ARTIVAtest2 = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
parentData = simulatedProfiles[parentGenes,],
targetName = targetGene,
parentNames = parentGenes,
segMinLength = 2,
edgesThreshold = 0.5,
niter = 20000,
outputPath = "ARTIVA-test")
## End(Not run)
Results
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> library(ARTIVA)
Loading required package: MASS
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ARTIVA/ARTIVAsubnet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ARTIVAsubnet
> ### Title: Function to recover Auto Regressive TIme-VArying interactions
> ### between a gene of interest (referred to as "target gene") and a set
> ### of genes which may explain the expression of the target gene.
> ### Aliases: ARTIVAsubnet
> ### Keywords: DBN inference network inference graphical model time series
>
> ### ** Examples
>
> # Load the ARTIVA R package
> library(ARTIVA)
>
> # Load the dataset with simulated gene expression profiles
> data(simulatedProfiles)
>
> # Name of the target gene to be analyzed with ARTIVA
> targetGene = 1
>
> # Names of the parent genes (typically transcription factors)
> parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")
>
> ###
> # ARTIVA analysis searching for potential interactions between the target
> # genes and a predefined list of parent genes.
> ###
>
> # Note that the number of iterations in the RJ-MCMC sampling is reduced
> # to in this example to 'niter=20000' (in order obtain a quick overview
> # of the ARTIVAnet fonction, but it should be increased (e.g. up to
> # 50000) for a better parameter estimation.
>
> # Without saving the output pictures "savePictures=FALSE"
> ## Not run:
> ##D ARTIVAtest = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
> ##D parentData = simulatedProfiles[parentGenes,],
> ##D targetName = targetGene,
> ##D parentNames = parentGenes,
> ##D segMinLength = 2,
> ##D edgesThreshold = 0.5,
> ##D niter = 20000,
> ##D savePictures=FALSE)
> ##D
> ##D # By default, the output results (pictures and estimation values) are
> ##D # saved in a folder named "ARTIVAsubnet" created in the current directory
> ##D ARTIVAtest = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
> ##D parentData = simulatedProfiles[parentGenes,],
> ##D targetName = targetGene,
> ##D parentNames = parentGenes,
> ##D segMinLength = 2,
> ##D edgesThreshold = 0.5,
> ##D niter = 20000)
> ##D
> ##D # In order to save the results in a specific folder, for example a
> ##D # folder entitled "ARTIVA-test" in the current directory:
> ##D
> ##D ARTIVAtest2 = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
> ##D parentData = simulatedProfiles[parentGenes,],
> ##D targetName = targetGene,
> ##D parentNames = parentGenes,
> ##D segMinLength = 2,
> ##D edgesThreshold = 0.5,
> ##D niter = 20000,
> ##D outputPath = "ARTIVA-test")
> ## End(Not run)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.