openCytoscape: Open cytoscape session with the network of miRNA-mRNA...

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

Description

Open cytoscape session and automatically load the network of miRNA-mRNA interactions.

Usage

openCytoscape(obj = NULL, pval.cutoff = 0.05, dat.sum =
                 obj@info[["dat.sum"]], file = NULL, cytoscape.folder =
                 "/home/mvila/Cytoscape_v2.8.3", sub.miRNA = NULL,
                 sub.mRNA = NULL, add.other = NULL, expand = FALSE)

Arguments

obj	a corObject
pval.cutoff	minimum corrected p value of selected miRNA-mRNA interactions
dat.sum	minimum ocurrences across databases of selected miRNA-mRNA interactions
file	name of the ".sif" network file that will be written. If NULL, file "network_default.sif" will be created
cytoscape.folder	path where "cytoscape.jar" file is located
sub.miRNA	character vector with the restricted miRNA
sub.mRNA	character vector with the restricted mRNA
add.other	other
expand	expand the network

References

http://cytoscape.org/

See Also

writeSif

Examples

##openCytoscape(data.obj)

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