Get GeneMANIA Edges

This function processes the GM results text file and returns it as a filtered edgelist.

Usage

GetGeneMANIA.edges(gm.results.path, gene.cccn.nodes)

Arguments

gm.results.path

Path to GeneMANIA results text file

gene.cccn.nodes

A list of nodes that are in the Gene CoCluster Correlation Network derived from common clusters between the three distance metrics (Euclidean, Spearman, and Combined (SED))

Value

Data frame of consisting of the network of interactions from the genes of study

Details

To get the GeneMANIA results text file, click on the three lines in the upper right corner. This should be under the GeneMANIA side window beside the species. Click "Export Results". The path to this file is the gm.results.path. An visual depiction of these instructions in the vignette PTMsToPathways under the GeneMANIA section.

Examples

ex.gm.results.path <- system.file("extdata/ex_gm_edgetable.csv", package = "PTMsToPathways")
example.GeneMANIA.edges <- GetGeneMANIA.edges(ex.gm.results.path, ex.gene.cccn.nodes)
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in start_line[1]:(end_line[1] - 1): NA/NaN argument
utils::head(example.GeneMANIA.edges)
#> Error: object 'example.GeneMANIA.edges' not found