expdata: Example data set

In c3net: Inferring Large-Scale Gene Networks with C3NET

Example data set

Description

expdata This data set has been generated by SynTRen. The source network corresponds to a subnetwork of E.coli (file name "EColi_full_HongWu_Ma_NAR2004.sif" from Ma HW, et. al. Nuc. Ac. Res. 2004).

Usage

data( expdata )

Arguments

expdata

Example data; rows correspond to variables (e.g. genes) and columns to samples.

Details

The example is also given to provide a sample data set so that one can take it as reference while formatting the new data set as entry to c3net. Data sets must be complete and no empty or non-numerical character allowed.

Value

expdata returns an example data set where rows are variables (e.g. genes) and columns are samples. It consists of 400 genes, 898 edges, and 800 steady-state samples.

References

Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP: An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res 2004 , 32:6643-6649

Bulcke, T.V., Leemput, K.V., Naudts, B., et. al. (2006) Syntren: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics, 7(1), 43.

G. Altay, F. Emmert-Streib, "Inferring the conservative causal core of gene regulatory networks", BMC Systems Biology (2010) 4:132.

See Also

c3, c3net, makemim

Examples

data(expdata)

c3net documentation built on June 24, 2022, 5:07 p.m.