Summary of a FAMTdata or a FAMTmodel

Description

The function produces summaries of 'FAMTdata' or 'FAMTmodel'. The function involves a specific method depending on the class of the main argument.

If the main argument is a 'FAMTdata' object, the function provides, for the 'expression file', the number of tests (which corresponds to the number of genes or rows), the sample size (which is the number of arrays or columns). The function provides classical summaries for 'covariates' and 'annotations' data (see summary in FAMT-package).

If the argument is a 'FAMTmodel', the function provides the numbers of rejected genes using classical and FAMT analyses, the annotation characteristics of significant genes, and the estimated proportion of true null hypotheses.

Usage

summaryFAMT(obj, pi0 = NULL, alpha = 0.15, info = c("ID", "Name"))

Arguments

Value

If the argument is a 'FAMTdata': a list with components expression:

If the argument is a 'FAMTmodel':

Author(s)

David Causeur

See Also

as.FAMTdata, modelFAMT

Examples

## Reading 'FAMTdata'
data(expression)
data(covariates)
data(annotations)
chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2)

## Summary of a 'FAMTdata'
#############################################
summaryFAMT(chicken)

## Summary of a 'FAMTmodel'
#############################################
# FAMT complete multiple testing procedure 
model = modelFAMT(chicken,x=c(3,6),test=6,nbf=3)
summaryFAMT(model)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FAMT)
Loading required package: mnormt
Loading required package: impute
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FAMT/summaryFAMT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summaryFAMT
> ### Title: Summary of a FAMTdata or a FAMTmodel
> ### Aliases: summaryFAMT
> 
> ### ** Examples
> 
> ## Reading 'FAMTdata'
> data(expression)
> data(covariates)
> data(annotations)
> chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2)
$`Rows with missing values`
integer(0)

$`Columns with missing values`
integer(0)

> 
> ## Summary of a 'FAMTdata'
> #############################################
> summaryFAMT(chicken)
$expression
$expression$`Number of tests`
[1] 9893

$expression$`Sample size`
[1] 43


$covariates
 AfClass   ArrayName        Mere    Lot         Pds9s            Af          
 F :18   F10    : 1   GMB05555:10   L2:16   Min.   :1994   Min.   :-25.5397  
 L :19   F11    : 1   GMB05625: 7   L3:11   1st Qu.:2284   1st Qu.: -8.0042  
 NC: 6   F12    : 1   GMB05562: 5   L4: 8   Median :2371   Median :  2.7166  
         F13    : 1   GMB05599: 5   L5: 8   Mean   :2370   Mean   :  0.2365  
         F14    : 1   GMB05554: 4           3rd Qu.:2474   3rd Qu.:  8.6037  
         F15    : 1   GMB05589: 4           Max.   :2618   Max.   : 18.1024  
         (Other):37   (Other) : 8                                            

$annotations
         ID      
 RIGG00001:   1  
 RIGG00002:   1  
 RIGG00003:   1  
 RIGG00005:   1  
 RIGG00006:   1  
 RIGG00007:   1  
 (Other)  :9887  
                                                                           Name     
 Weakly similar to Q95JC9 (Q95JC9) Basic proline-rich protein                :  11  
 No Match                                                                    :   8  
 Weakly similar to Q90811 (Q90811) Hypothetical 28.6 kDa protein (Fragment)  :   8  
 Weakly similar to Q9DDJ7 (Q9DDJ7) Retinoblastoma tumor suppressor (Fragment):   8  
 Weakly similar to Q08525 (Q08525) Reverse transcriptase                     :   6  
 Weakly similar to Q8MW53 (Q8MW53) Precollagen-D                             :   6  
 (Other)                                                                     :9846  
     Block           Column           Row            Length     
 Min.   : 1.00   Min.   : 1.00   Min.   : 1.00   Min.   :60.00  
 1st Qu.:13.00   1st Qu.: 6.00   1st Qu.: 6.00   1st Qu.:70.00  
 Median :25.00   Median :11.00   Median :12.00   Median :70.00  
 Mean   :24.87   Mean   :11.04   Mean   :11.63   Mean   :69.57  
 3rd Qu.:37.00   3rd Qu.:16.00   3rd Qu.:17.00   3rd Qu.:70.00  
 Max.   :48.00   Max.   :21.00   Max.   :22.00   Max.   :75.00  
                                                                

> 
> ## Summary of a 'FAMTmodel'
> #############################################
> # FAMT complete multiple testing procedure 
> model = modelFAMT(chicken,x=c(3,6),test=6,nbf=3)
[1] "Fitting Factor Analysis Model with 3 factors"
[1] "Fitting Factor Analysis Model with 3 factors"
> summaryFAMT(model)
$nbreject
  alpha Raw analysis FA analysis
1  0.15            0           6

$DE
            ID
6722 RIGG05436
3885 RIGG04393
1119 RIGG15056
3484 RIGG05478
463  RIGG09893
124  RIGG12578
                                                                           Name
6722                                                           Same gene X54200
3885             Weakly similar to CAE03429 (CAE03429) OSJNBa0032F06.12 protein
1119                                                       ENSGALT00000015290.1
3484 Weakly similar to Q8IUG4 (Q8IUG4) Rho GTPase activating protein (Fragment)
463                                                        ENSGALT00000000452.1
124                                                        ENSGALT00000008042.1

$pi0
[1] 0.9738531

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>