summary: Summarize an msets Object

Description Usage Arguments Value Author(s) References See Also Examples

Description

This function outputs summary statistics of a msets object.

Usage

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## S3 method for class '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.

Author(s)

Minghui Wang <[email protected]>, Bin Zhang <[email protected]>

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

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## 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)

## End(Not run)

Example output

Loading required package: grid

Attaching package: 'SuperExactTest'

The following objects are masked from 'package:base':

    intersect, union

A msets object with 4 sets: S1 S2 S3 S4 
Background size: 26 
Summary of intersections:
         Intersections Degree Observed.Overlap Expected.Overlap        FE
0001                S4      1               10               NA        NA
0010                S3      1               10               NA        NA
0011           S3 & S4      2                4         3.846154 1.0400000
0100                S2      1               17               NA        NA
0101           S2 & S4      2                6         6.538462 0.9176471
0110           S2 & S3      2                7         6.538462 1.0705882
0111      S2 & S3 & S4      3                3         2.514793 1.1929412
1000                S1      1               20               NA        NA
1001           S1 & S4      2                9         7.692308 1.1700000
1010           S1 & S3      2                7         7.692308 0.9100000
1011      S1 & S3 & S4      3                4         2.958580 1.3520000
1100           S1 & S2      2               11        13.076923 0.8411765
1101      S1 & S2 & S4      3                5         5.029586 0.9941176
1110      S1 & S2 & S3      3                4         5.029586 0.7952941
1111 S1 & S2 & S3 & S4      4                3         1.934456 1.5508235
       P.value                 Elements
0001        NA b, d, f, g, k, l, m, ...
0010        NA a, c, d, k, l, m, t, ...
0011 0.6094764               d, k, l, m
0100        NA j, k, l, m, n, o, p, ...
0101 0.8107343         k, l, m, p, r, y
0110 0.5171625      k, l, m, t, u, x, z
0111 0.4909272                  k, l, m
1000        NA a, b, c, d, e, f, g, ...
1001 0.2245059 b, d, f, g, k, l, m, ...
1010 0.8721192      a, c, d, k, l, m, t
1011 0.3202667               d, k, l, m
1100 1.0000000 j, k, l, m, n, o, p, ...
1101 0.6571502            k, l, m, p, r
1110 0.8802423               k, l, m, t
1111 0.2907561                  k, l, m

SuperExactTest documentation built on Feb. 9, 2018, 6:08 a.m.