writeSif: Write a SIF file

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Export the network (from cytofile slot) to a SIF file.

Usage

writeSif(obj, file, pval.cutoff = 0.05, cor = NULL, alternative = "less",
        dat.sum = obj@info[["dat.sum"]], add.other = NULL, sub.miRNA = NULL,
        sub.mRNA = NULL, expand = FALSE, vertex.cex = "interact.table")

Arguments

obj	a corObject.
file	file to write.
pval.cutoff	maximum corrected p value to take.
cor	correlation cutoff.
alternative	"less": select correlations lower than correlation cutoff; "greater": select correlations greater than correlation cutoff; or "two.sided": select correlations with absolute value greater than correlation cutoff.
dat.sum	number of minimum ocurrences across databases
add.other	a character vector. Name of the dataframe that contains extra interactions (usually mRNA-mRNA interactions) that will be added to the network.
sub.miRNA	character vector. Restrict to these miRNAs.
sub.mRNA	character vector. Restrict to these mRNAs.
expand	expand with another table. TRUE or FALSE.
vertex.cex	table to use to expand

Value

A sif file, plus a node attributes file (*the node attributes still in preparation)

References

www.cytoscape.org

See Also

writeCsv, writeSif, selSubsetCor, selSubsetExprs, openCytoscape

Examples

## do not run
#data(data.obj)
#writeSif(data.obj,"results_sif")

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.