writeSif: Write a SIF file

Description Usage Arguments Value References See Also Examples

View source: R/functions.R

Description

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

Usage

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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

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

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