Enrichment score

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Description

Calculates an enrichment score for a gene set.

Usage

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es(L, S, p = 1, doplot = FALSE, index = FALSE)

Arguments

L

Vector with one expression value per gene.

S

Vector of same length as L where 1 indicates that the gene in L is present in the gene set and 1 indicates that it is not.

p

Weight. Default is 1.

doplot

If TRUE, the running sum is plotted. Default is FALSE.

index

If TRUE, the index at which the ES occurs in the sorted list is returned. Default is FALSE.

Details

See Subramanian et al. for details.

Value

E

Enrichment score.

ind

Index of the enrichment score (if index=TRUE).

Author(s)

Guro Dorum

References

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. and Mesirov, J. P (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression pro?les, PNAS, 102, 15545-15550.

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.