selectGeneSets {sigPathway} | R Documentation

## Select gene sets to be analyzed in 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

[Package sigPathway version 1.12.1 Index]