qpTopPairs {qpgraph} | R Documentation

## Report pairs of variables

### Description

Report a top number of pairs of variables according to either some association measure and/or occurring in a given reference graph.

### Usage

    qpTopPairs(measurementsMatrix=NULL, refGraph=NULL, n=6L, file=NULL,
               decreasing=FALSE, pairup.i=NULL, pairup.j=NULL,
               annotation=NULL, fcOutput=NULL, fcOutput.na.rm=FALSE,
               digits=NULL)

### Arguments

`measurementsMatrix` | matrix containing the measure of association between all pairs of variables.
`refGraph` | a reference graph containing the pairs that should be reported and provided either as an adjacency matrix, a `graphNEL-class` object or a `graphAM-class` object.
`n` | number of pairs to report, 6 by default, use `Inf` for reporting all of them.
`file` | file name to dump the pairs information as tab-separated column text.
`decreasing` | logical; if TRUE then the measurements are employed to be ordered in decreasing order; if FALSE then in increasing order.
`pairup.i` | subset of vertices to pair up with subset `pairup.j`.
`pairup.j` | subset of vertices to pair up with subset `pairup.i`.
`annotation` | name of an annotation package to transform gene identifiers into gene symbols when variables correspond to genes.
`fcOutput` | output of `qpFunctionalCoherence`.
`fcOutput.na.rm` | flag set to TRUE when pairs with `NA` values from `fcOutput` should not be reported; `FALSE` (default) otherwise.
`digits` | number of decimal digits reported in the values of `measurementsMatrix` and functional coherence values. By default `digits=NULL`, and therefore, no rounding is performed.

### Details

The `measurementsMatrix` should be symmetric and may have also contain `NA` values which will not be taken into account. That is an alternative way to restricting the variable pairs with the parameters `pairup.i` and `pairup.j`. The same holds for `refGraph`. One of these two, should be specified.

### Value

The ranking of pairs is invisibly returned.

### Author(s)

R. Castelo

### See Also

`qpGraph` `qpPrecisionRecall` `qpFunctionalCoherence`

### Examples

    qpTopPairs(matrix(runif(100), nrow=10, dimnames=list(1:10,1:10)))

[Package qpgraph version 2.16.0 Index]