CytoscapeFilter: CytoscapeFilter

In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Description

Reduces the size of a file intended for Cytoscape by filtering out the genes/clusters which are not correlated

Usage

CytoscapeFilter(cytoscape.file, threshold = 0.9, save = TRUE, filename = NULL)

Arguments

cytoscape.file	A dataframe object generated by CytoscapeFile
threshold	Positive genes below this threshold and negative genes above the additive inverse of this threshold will be removed.
save	Logical. If TRUE then the dataframe will be saved as a csv file.
filename	String. The name for the saved file.

Examples

filter.df <- CombiFilter(Laurasmappings)
pam.df <- PamClustering(filter.df, k = 10)
cor.df <- CorAnalysisClusterDataset(pam.df, save=FALSE)
cyto.df <- CytoscapeFile(cor.df, save = FALSE)
cyto.filtered.df <- CytoscapeFilter(cyto.df, threshold=0.95)

nathansam/CircadianTools documentation built on Dec. 26, 2019, 11:30 a.m.