Usage
ARTIVAsubnetAnalysis(ARTIVAsubnet=NULL, CPpostDist=NULL, CPsamples=NULL,
coefSamples=NULL, TFnumber=NULL, segMinLength=2, edgesThreshold=0.5,
burn_in=NULL, CPpos=NULL,targetData=NULL, parentData=NULL,
targetName=NULL,parentNames=NULL, savePictures=TRUE,saveEstimations=TRUE,
outputPath=NULL,layout="fruchterman.reingold", silent=FALSE,
inARTIVAsubnet=FALSE , onepage= FALSE)
Arguments
ARTIVAsubnet
Ouput of function ARTIVAsubnet, a list containing Samples,
Counters, CPpostDist, nbSegs,
SegmentPostDist, network, ...
(optional, default: ARTIVAsubnet=NULL, if
ARTIVAsubnet=NULL then parameters CPpostDist,
CPsamples, coefSamples, TFnumber must be not null.
CPpostDist
A list of 2 tables :
1)CPpostDist$CPnumberPostDist: A table containing the distribution for
the number of CPs approximated with ARTIVAsubnet.
2)CPpostDist$CPpositionPostDist: A table containing the distribution for the position of the CPs approximated with ARTIVAsubnet.
(optional, default: CPpostDist=NULL, but
CPpostDist must be given when parameter ARTIVAsubnet=NULL) CPsamples
A matrix with the different iterations (in row)
performed with the ARTIVAsubnet function and in column the identified positions for CPs. (optional, default: CPsamples=NULL, but
CPsamples must be given when parameter ARTIVAsubnet=NULL)
coefSamples
A matrix with the different (in row)performed with
the ARTIVAsubnet function and in column the
coefficient values corresponding to the identified regulatory interactions.
(optional, default: coefSamples=NULL, but
coefSamples must be given when parameter ARTIVAsubnet=NULL) TFnumber
Number of parent genes in the data
parentData used in the ARTIVAsubnet function.
(optional, default: TFnumber=NULL, but
TFnumber must be given when parameter ARTIVAsubnet=NULL) 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).
edgesThreshold
Probability threshold for the selection of the
edges of the time-varying regulatory network when
segmentAnalysis=TRUE (optional, default: edgesThreshold=0.5).
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).
CPpos
A table containing the desired most significant CP positions (optional, default:
CPpos=NULL, if CPpos=NULL then CPpos is
evaluated as in CP.postDist function. )
targetData
A vector with the temporal gene expression measurements for the
target gene (i.e. the gene whose regulation factors are looked
for). (optional, default: targetData=NULL, if not null then
the target data is plotted).
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. (optional, default: parentData=NULL, if not null then
the parent data is plotted).
targetName
Name of the target gene (optional, default: targetName="Target").
parentNames
A vector with the names for parent gene(s) (optional, default: parentNames=NULL).
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).
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).
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).
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").
silent
Boolean, if TRUE messages are printed along the ARTIVA procedure (optional, default: silent=FALSE).
inARTIVAsubnet
Boolean, if TRUE, general information already printed in
function ARTIVAsubnet are not printed a second time (optional, default: inARTIVAsubnet=FALSE).
onepage
Boolean, if TRUE, all output pictures are plotted on one page
only (optional, default: onepage=FALSE.