Significance level computation in GSEA

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Description

Ccomputes a p-value for a gene set.

Usage

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significance(ES, ESnull, doplot = FALSE)

Arguments

ES

Observed enrichment score.

ESnull

Null distribution.

doplot

If TRUE, a histogram over the normalised null distribution is drawn. Default is FALSE.

Details

Function that computes a p-value for a gene set given an enrichment score and a null distribution. Calculations are done separately for positive and negative enrichment scores. The function also returns normalised observed enrichment score and normalised null distribution for the gene set. In addition, a histogram over the normalised null distribution can be plotted.

Value

p.value

p-value for the gene set.

NES

Normalised observed enrichment score.

NESnull

Normalised estimated null distribution.

Author(s)

Guro D\orum

Examples

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

## The function is currently defined as