supertest {SuperExactTest}

Calculate Intersections Among Multiple Sets and Perform Statistical Tests

Description

This function calculates intersection sizes among multiple sets and performs statistical tests of the intersections.

Usage

supertest(x, n=NULL, degree=NULL, ...)

Arguments

x

list; a collection of sets.

n

integer, background population size. Required for computing the statistical significance of intersections.

degree

a vector of intersection degrees for overlap analysis. E.g., when degree=c(2:3), only those intersections involving two or three sets will be computed. By default, degree=NULL, all possible intersections are computed.

...

additional arguments (not implemented).

Details

This function calculates intersection sizes between multiple sets and, if background population size n is specified, performs statistical tests of the intersections. For a brief introduction of using this package, please see vignette("set_html").

Value

An object of class msets.

Author(s)

Minghui Wang <[e-mail]>, Bin Zhang <[e-mail]>

References

Minghui Wang, Yongzhong Zhao, and Bin Zhang (2015). Efficient Test and Visualization of Multi-Set Intersections. Scientific Reports 5: 16923.

See Also

msets, MSET, Cancer, cpsets, dpsets

Examples

## Not run: 
#Analyze the cancer gene sets
data(Cancer)
Result=supertest(Cancer, n=20687)
summary(Result)
plot(Result,degree=2:7,sort.by='size')

## End(Not run)