summarize: Summarize the object of S4 class 'BetaMixture' or 'PAN'

In PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Description

The function helps print a summary of an object of S4 class BetaMixture or PAN.

Usage

summarize(object, what='ALL', ...) 

Arguments

object	an object of S4 class BetaMixture or PAN.
what	a character value specifying what to print (see details).
...	not in use, only for further extension.

Details

This function print a summary of an object of BetaMixture or PAN. The function is also called by S4 method show, which prints only a short message about the input parameters and data.

For an object of class BetaMixture:

If what='input', the function prints to screen a summary of input parameters; If what='fitNULL', the function prints to screen a summary of fitting results for the NULL distribution. If what='fitBM', the function prints to screen a summary of fitting results for the beta-mixture model. If what='ALL', all above messages will be printed.

For an object of class PAN:

If what='input', the function prints to screen a summary of input object(s) of class BetaMixture; If what='graph', the function prints to screen a summary of inferred posterior association network; If what='module', the function prints to screen a summary of functional gene modules; If what='ALL', all above messages will be printed.

Author(s)

Xin Wang [e-mail]

References

Xin Wang, Mauro Castro, Klaas W. Mulder and Florian Markowetz, Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, in preparation.

Examples

data(bm)
summarize(bm1, what='ALL')

Example output

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union


-input 
phenotype partition     model    metric 
  273 x 7      None    global    cosine 

-NULL fitting 
           No. of perm       summarize method     permutation method 
                    10                 median                    all 
shape1 (start->fitted) shape2 (start->fitted) 
              4->2.990               4->2.938 

-Beta-Mixture model fitting
--parameters: 
                 z (init)            shapes(- init)            shapes(x init) 
                     None        shape1=2, shape2=4 shape1=2.99, shape2=2.990 
           shapes(+ init)                     gamma 
       shape1=4, shape2=2                      None 
--control arguments: 
     fitNULL    tolerance maxIteration 
       FALSE          0.1          Inf 
--results: 
           shapes(- fitted)            shapes(x fitted) 
shape1=3.031, shape2=11.404  shape1=2.990, shape2=2.938 
           shapes(+ fitted)                 pi (fitted) 
 shape1=8.429, shape2=1.650           0.260,0.491,0.249 
                        NLL 
                  16749.304 

PANR documentation built on Nov. 8, 2020, 8:15 p.m.