Select gene sets to be analyzed in pathway analysis

Share:

Description

Selects gene sets to be analyzed in pathway analysis based on minimum and maximum number of probe sets to consider per pathway.

Usage

1
selectGeneSets(G, probeID, minNPS = 20, maxNPS = 500)

Arguments

G

a list containing the source, title, and probe sets associated with each curated pathway

probeID

a character vector containing the names of probe sets associated with a matrix of expression values

minNPS

an integer specifying the minimum number of probe sets in probeID that should be in a gene set

maxNPS

an integer specifying the maximum number of probe sets in probeID that should be in a gene set

Details

This function selects the appropriate pathways from a large, curated list based on the minimum and maximum number of probe sets that should be considered in a gene set. It creates three vectors: nprobesV and indexV representing a sparse indicator matrix and indGused indicating which gene sets were selected from G.

Value

A list containing

nprobesV

an integer vector indicating the number of probe sets in probeID that is in each selected gene set

indexV

an integer vector containing positions for each 1s in the sparse indicator matrix

indGused

an integer vector indicating which pathways in G were chosen

Note

See the help page for calculate.NTk or calculate.NEk for example code that uses getPathwayStatistics

Author(s)

Lu Tian, Peter Park, and Weil Lai

References

Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S., Park P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the USA, 102, 13544-9.

http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102