neat (version 1.2.4)

summary.neat: Summary method of neat

Description

summary method for class "neat".

Usage

# S3 method for neat
summary(object, ...)

Value

The summary.neat function returns the following values:

• the number of tests computed;

• the number of enrichments at 1% and 5% level;

• the p-value of the Kolmogorov-Smirnov test to check if the distribution of p-values is uniform.

Arguments

object

An object of class "neat"

...

Further arguments passed to or from other methods

Author

Mirko Signorelli

References

Signorelli, M., Vinciotti, V., Wit, E. C. (2016). NEAT: an efficient network enrichment analysis test. BMC Bioinformatics, 17:352. Url: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1203-6.

See Also

neat, plot.neat, summary.neat

Examples

if (FALSE) {
data(yeast)
esr = list('ESR 1' = yeast$esr1, 'ESR 2' = yeast$esr2)
test = neat(alist = esr, blist = yeast$goslimproc, network = yeast$yeastnet,
            nettype = 'undirected', nodes = yeast$ynetgenes, alpha = 0.01)

test1 = test[1:99,]
summary(test1)

test2 = test[100:198,]
summary(test2)
}