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)

Arguments

tab a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
phenotype a numeric 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

Details

This function 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)

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 and Peter Park, with contributions from 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 1.1-0 Index]