qpTopPairs: Report pairs of variables

In rcastelo/qpgraph: Estimation of genetic and molecular regulatory networks from high-throughput genomics data

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)))

rcastelo/qpgraph documentation built on Oct. 28, 2024, 5:15 a.m.