Gene annotations data frame

Description

A data frame with 6 columns describing the 9893 genes, which expressions are stored in the 'expression' dataset, in terms of functional categories, oligonucleotide size and location on the microarray. See also expression, covariates.

Usage

data(annotations)

Format

A data frame with 9893 observations on the following 6 variables.

ID

Gene identification

Name

Gene annotation (functional categories) (character)

Block

Location on the microarray(factor)

Column

Location on the microarray (factor)

Row

Location on the microarray (factor)

Length

Oligonucleotide size (numeric vector)

Source

UMR Genetique Animale - INRA/AGROCAMPUS OUEST - Rennes, France.

References

Blum Y., Le Mignon G., Lagarrigue S. and Causeur S. (2010) - A factor model to analyze heterogeneity in gene expression, BMC Bioinformatics, 11:368.

Le Mignon, G. and Desert, C. and Pitel, F. and Leroux, S. and Demeure, O. and Guernec, G. and Abasht, B. and Douaire, M. and Le Roy, P. and Lagarrigue S. (2009) - Using trancriptome profling to characterize QTL regions on chicken chromosome 5. BMC Genomics, 10:575.

Examples

data(annotations)
dim(annotations) 
summary(annotations)

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/annotations.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotations
> ### Title: Gene annotations data frame
> ### Aliases: annotations
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(annotations)
> dim(annotations) 
[1] 9893    6
> summary(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  
                                                                
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>