qunetwork {QUBIC} | R Documentation

## Construction and visualization of co-expression network

### Description

This function can automatically create co-expression networks along with their visualization based on identified biclusters in QUBIC. Three correlation methods, Pearson, Kendall and Spearman, are available for a user, facilitating different preferences in practical usage.

### Usage

    qunetwork(x, BicRes, number = 1:BicRes@Number, groups = c(number[[1]]),
      method = c("pearson", "kendall", "spearman"))

### Arguments

`x` | The data matrix
`BicRes` | biclust::BiclustResult object
`number` | Which bicluster to be plotted
`groups` | An object that indicates which nodes belong together.
`method` | A character string indicating which correlation coefficient (or covariance) is to be computed. One of 'pearson' (default), 'kendall', or 'spearman', can be abbreviated.

### Value

a list contains a weights matrix and groupinfo

### See Also

`qunet2xml` `QUBIC` `cor`

### Examples

    # Load microarray matrix
    data(BicatYeast)
    res <- biclust::biclust(BicatYeast[1:50, ], method=BCQU(), verbose = FALSE)
    # Constructing the networks for the 4th and 13th identified biclusters.
    net <- qunetwork(BicatYeast[1:50, ], res, number = c(4, 13), group = c(4, 13), method = 'spearman')
    ## Not run:
    if (requireNamespace('qgraph'))
        qgraph::qgraph(net[[1]], groups = net[[2]], layout = 'spring', minimum = 0.6,
           color = cbind(rainbow(length(net[[2]]) - 1),'gray'), edge.label = FALSE)

    ## End(Not run)
    ## Not run:
    #Load microarray matrix
    data(BicatYeast)
    res <- biclust::biclust(BicatYeast[1:50, ], method=BCQU(), verbose = FALSE)
    # Constructing the networks for the 4th and 13th identified biclusters,
    #   using the whole network as a background.
    net <- qunetwork(BicatYeast[1:50, ], res, group = c(4, 13), method = 'spearman')
    if (requireNamespace('qgraph'))
        qgraph::qgraph(net[[1]], groups = net[[2]], layout = 'spring', minimum = 0.6,
           color = cbind(rainbow(length(net[[2]]) - 1),'gray'), edge.label = FALSE)

    ## End(Not run)

[Package QUBIC version 1.15.1 Index]