summary.neat: Summary method of 'neat'

In neat: Efficient Network Enrichment Analysis Test

Description

summary method for class "neat".

Usage

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

Arguments

object	An object of class "neat"
...	Further arguments passed to or from other methods

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.

Author(s)

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

## Not run: 
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)

## End(Not run)

neat documentation built on Jan. 7, 2021, 9:09 a.m.