qpPCC {qpgraph} | R Documentation

## Estimation of Pearson correlation coefficients

### Description

Estimates Pearson correlation coefficients (PCCs) and their corresponding P-values between all pairs of variables from an input data set.

### Usage

    ## S4 method for signature 'ExpressionSet'
    qpPCC(X)
    ## S4 method for signature 'data.frame'
    qpPCC(X, long.dim.are.variables=TRUE)
    ## S4 method for signature 'matrix'
    qpPCC(X, long.dim.are.variables=TRUE)

### Arguments

`X` | data set from where to estimate the Pearson correlation coefficients. It can be an ExpressionSet object, a data frame or a matrix.
`long.dim.are.variables` | logical; if TRUE it is assumed that when `X` is a data frame or 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.

### Details

The calculations made by this function are the same as the ones made for a single pair of variables by the function `cor.test` but for all the pairs of variables in the data set, with the exception of the treatment of missing values, since only complete observations across all variables in `X` are used.

### Value

A list with two matrices, one with the estimates of the PCCs and the other with their P-values.

### Author(s)

R. Castelo and A. Roverato

### See Also

`qpPAC`

### Examples

    require(graph)
    require(mvtnorm)

    nVar <- 50 ## number of variables
    nObs <- 10 ## number of observations to simulate

    set.seed(123)

    g <- randomEGraph(as.character(1:nVar), p=0.15)

    Sigma <- qpG2Sigma(g, rho=0.5)
    X <- rmvnorm(nObs, sigma=as.matrix(Sigma))

    pcc.estimates <- qpPCC(X)

    ## get the corresponding boolean adjacency matrix
    A <- as(g, "matrix") == 1

    ## Pearson correlation coefficients of the present edges
    summary(abs(pcc.estimates$R[upper.tri(pcc.estimates$R) & A]))

    ## Pearson correlation coefficients of the missing edges
    summary(abs(pcc.estimates$R[upper.tri(pcc.estimates$R) & !A]))

[Package qpgraph version 2.20.0 Index]