SuperExactTest (version 1.0.7)

summary.msets: Summarize an msets Object

Description

This function outputs summary statistics of a msets object.

Usage

# S3 method for msets
summary(object, degree=NULL, ...)

Arguments

object

a msets object.

degree

a vector of intersection degrees to pull out.

...

additional arguments (not implemented).

Value

A list:

Barcode

a vector of 0/1 character strings, representing the set composition of each intersection.

otab

a vector of observed intersection size between any combination of sets.

etab

a vector of expected intersection size between any combination of sets if background population size is specified.

set.names

set names.

set.sizes

set sizes.

n

background population size.

P.value

upper tail p value for each intersection if background population size n is specified.

Table

a data.frame containing degree, otab, etab, fold change, p value and the overlap elements.

References

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

See Also

msets

Examples

# NOT RUN {
#set up fake data
x=list(S1=letters[1:20], S2=letters[10:26], S3=sample(letters,10), S4=sample(letters,10))
obj=supertest(x,n=26)
summary(obj)
# }