graphite (version 1.18.0)

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 PathwayList object or a list of Pathways.

pathwaySetName

name of the output pathway set.

print.names

print pathway names as the conversion advances.

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

spia

PathwayList