calculate.GSEA {sigPathway} | R Documentation

## Calculate 2-sided statistics based on the GSEA algorithm

### Description

Calculates the 2-sided statistics based on the GSEA algorithm.

### Usage

    calculate.GSEA(tab, phenotype, gsList, nsim = 1000,
                   verbose = FALSE, alwaysUseRandomPerm = FALSE)

### Arguments

`tab` | a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
`phenotype` | a numeric or character vector indicating the phenotype
`gsList` | a list containing three vectors from the output of the `selectGeneSets` function
`nsim` | an integer indicating the number of permutations to use
`verbose` | a boolean to indicate whether to print debugging messages to the R console
`alwaysUseRandomPerm` | a boolean to indicate whether the algorithm can use complete permutations for cases where `nsim` is greater than the total number of unique permutations possible with the `phenotype` vector

### Details

This function assumes 2 distinct types of phenotypes in the data. It calculates a variant of the GSEA statistics (Mootha et al.) with the following modifications: (a) GSEA was changed from a 1-sided to a 2-sided approach. (b) The 2-group t-statistics is used as the difference metric.

The function also normalizes the GSEA statistic and calculates the corresponding q-values for each gene set as described in Tian et al. (2005) The function's output can be used for further analysis in other functions such as `rankPathways.NGSk` or `getPathwayStatistics.NGSk`.

### Value

A list containing

`ngs` | number of gene sets
`nsim` | number of permutations performed
`t.set` | a numeric vector of Tk statistics
`t.set.new` | a numeric vector of NTk statistics
`p.null` | the proportion of nulls
`p.value` | a numeric vector of p-values
`q.value` | a numeric vector of q-values

### Author(s)

Lu Tian, Peter Park, and Weil Lai

### References

Mootha V.K., Lindgren C.M., Eriksson K.F., Subramanian A., Sihag S., Lehar J., Puigserver P., Carlsson E., Ridderstrale M., Laurila E., Houstis N., Daily M.J., Patterson N., Mesirov J.P., Golud T.R., Tamayo P., Spiegelman B., Lander E.S., Hirshhorn J.N., Altshuler D., Groop L.C. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature Genetics, 34, 267-73.

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 1.4.0 Index]