selectGeneSets: Select gene sets to be analyzed in pathway analysis

In sigPathway: Pathway Analysis

Description

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

Usage

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

sigPathway documentation built on Nov. 8, 2020, 5:35 p.m.