graphite (version 1.12.0)

prepareSPIA: Prepare pathway dataset needed by runSPIA.

Description

Prepare pathway dataset needed by runSPIA. See runSPIA and spia for more details.

Usage

prepareSPIA(db, pathwaySetName, print.names = FALSE)

Arguments

db

A list of pathways like biocarta, kegg,nci or reactome.

pathwaySetName

Name of the pathway set in output.

print.names

The verbose option.

Details

It is required to run this function before runSPIA to prepare the pathway set as required by runSPIA.

References

Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009 Jan 1;25(1):75-82.

Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82.

Draghici, S., Khatri, P., Tarca, A.L., Amin, K., Done, A., Voichita, C., Georgescu, C., Romero, R.: A systems biology approach for pathway level analysis. Genome Research, 17, 2007.

See Also

runSPIA