qpAllCItests {qpgraph} | R Documentation

## Tests of conditional independence

### Description

Performs a test of conditional independence for every pair of variables.

### Usage

    ## S4 method for signature 'matrix'
    qpAllCItests(X, I=NULL, Q=NULL, pairup.i=NULL, pairup.j=NULL,
                                    long.dim.are.variables=TRUE, exact.test=TRUE,
                                    use=c("complete.obs", "em"), tol=0.01,
                                    return.type=c("p.value", "statn", "all"), verbose=TRUE,
                                    R.code.only=FALSE, clusterSize=1, estimateTime=FALSE,
                                    nAdj2estimateTime=10)

### Arguments

`X` | data set from where to estimate the non-rejection rates. It can be an ExpressionSet object, a data frame or a matrix.
`I` | indexes or names of the variables in `X` that are discrete. See details below regarding this argument.
`Q` | indexes or names of the variables in `X` forming the conditioning set.
`pairup.i` | subset of vertices to pair up with subset `pairup.j`
`pairup.j` | subset of vertices to pair up with subset `pairup.i`
`long.dim.are.variables` | logical; if `TRUE` it is assumed that when data are in a data frame or in a matrix, the longer dimension is the one defining the random variables (default); if `FALSE`, then random variables are assumed to be at the columns of the data frame or matrix.
`exact.test` | logical; if `FALSE` an asymptotic conditional independence test is employed with mixed (i.e., continuous and discrete) data; if `TRUE` (default) then an exact conditional independence test with mixed data is employed. See details below regarding this argument.
`use` | a character string defining the way in which calculations are done in the presence of missing values. It can be either `"complete.obs"` (default) or `"em"`.
`tol` | maximum tolerance controlling the convergence of the EM algorithm employed when the argument `use="em"`.
`return.type` | type of value returned by this function. By default `"p.value"` indicates that a list containing a matrix of p-values from all performed conditional independence (CI) tests will be returned. If `return.type="statn"` then a list containing the matrix of the statistics and the sample sizes on each CI test, will be returned. If `return.type="all"` then all previous matrices of values will be returned within a list.
`verbose` | show progress on the calculations.
`R.code.only` | logical; if `FALSE` then the faster C implementation is used (default); if `TRUE` then only R code is executed.
`clusterSize` | size of the cluster of processors to employ if we wish to speed-up the calculations by performing them in parallel. A value of 1 (default) implies a single-processor execution. The use of a cluster of processors requires having previously loaded the packages `snow` and `rlecuyer`.
`estimateTime` | logical; if `TRUE` then the time for carrying out the calculations with the given parameters is estimated by calculating for a limited number of adjacencies, specified by `nAdj2estimateTime`, and extrapolating the elapsed time; if `FALSE` (default) calculations are performed normally till they finish.
`nAdj2estimateTime` | number of adjacencies to employ when estimating the time of calculations (`estimateTime=TRUE`). By default this has a default value of 10 adjacencies and larger values should provide more accurate estimates. This might be relevant when using a cluster facility.

### Details

When `I` is set different to `NULL` then mixed graphical model theory is employed and, concretely, it is assumed that the data comes from an homogeneous conditional Gaussian distribution. By default, with `exact.test=TRUE`, an exact test for conditional independence is employed, otherwise an asymptotic one will be used. Full details on these features can be found in Tur, Roverato and Castelo (2014).

### Value

A list with three entries called `p.value`, `statistic` and `n` corresponding to a `dspMatrix-class` symmetric matrix of p-values for the null hypothesis of coindtional independence with the diagonal set to `NA` values, an analogous matrix of the statistics of each test and of the sample sizes, respectively. These returned values, however, depend on the setting of argument `return.type` which, by default, enables only returning the matrix of p-values. If arguments `pairup.i` and `pairup.j` are employed, those cells outside the constrained pairs will get also a `NA` value.

Note, however, that when `estimateTime=TRUE`, then instead of the matrix of estimated non-rejection rates, a vector specifying the estimated number of days, hours, minutes and seconds for completion of the calculations is returned.

### Author(s)

R. Castelo, A. Roverato and I. Tur

### References

Castelo, R. and Roverato, A. A robust procedure for Gaussian graphical model search from microarray data with p larger than n, J. Mach. Learn. Res., 7:2621-2650, 2006.

Tur, I., Roverato, A. and Castelo, R. Mapping eQTL networks with mixed graphical Markov models. Genetics, 198:1377-1393, 2014.

### See Also

`qpCItest`

### Examples

    library(mvtnorm)

    nVar <- 50  ## number of variables
    maxCon <- 3 ## maximum connectivity per variable
    nObs <- 30  ## number of observations to simulate

    set.seed(123)

    A <- qpRndGraph(p=nVar, d=maxCon)
    Sigma <- qpG2Sigma(A, rho=0.5)
    X <- rmvnorm(nObs, sigma=as.matrix(Sigma))

    alltests <- qpAllCItests(X, verbose=FALSE)

    ## distribution of p-values for the present edges
    summary(alltests$p.value[upper.tri(alltests$p.value) & A])

    ## distribution of p-values for the missing edges
    summary(alltests$p.value[upper.tri(alltests$p.value) & !A])

[Package qpgraph version 2.20.0 Index]