How Can I Read The Contents Of Rdata!, Where Is It Located ? And How Can I Access It?

Question

[Zhongshan]

Hi, dear members. I faced a problem when I used R package TIGRE. Because the Rdata stored in the package is about Drosophila. I really want to have a look about its data structure; in this way, I can figure out how to form my annotation or other necessary data types, and input my microarray data, which is about a plant pathogen, Gibberella zeae, different from the insect Drosophila. As the I don't manually annotated the genome of our fungus, so I want to input my annotation file into R and combine this file with my microarray file, then I can carry out transcription factor target identifications. Would do you please give me some suggestions? Thanks

The following is the results of R, and I really want to know the structure of the data drosophila_gpsim_fragment.

> library(tigre)

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.
> data(drosophila_gpsim_fragment)
> drosophila_gpsim_fragment

ExpressionTimeSeries (storageMode: lockedEnvironment)
assayData: 4 features, 36 samples 
  element names: exprs, var.exprs 
phenoData
  sampleNames: embryo_tc_4_1.CEL, embryo_tc_4_2.CEL, ..., embryo_tc_8_12.CEL  (36 total)
  varLabels and varMetadata description:
    time.h: time.h
    experiments: experiment ID
    modeltime: modeltimes
featureData
    featureNames: 143396_at, 148227_at, 152715_at, 147995_at
    fvarLabels and fvarMetadata description: none

experimentData: use 'experimentData(object)'
Annotation: drosgenome1

Answer 1

[Chris Miller]

Have you tried the str() command? It will let you examine the structure of an object.

Answer 2

[Zhongshan]

I have to learn R more, then maybe I can solve this problem later

Answer 3

[Pierre Lindenbaum]

I'm not sure about what kind of data are your 'RData'.

However is your data are some R variables that have been serialized, the C source code for reading this kind of file is available here.

[Zhongshan]

Ok. Thanks, unfortunately, I don't know how to run this C code, because of my totally blind of the language C.

Answer 4

[Brad Chapman]

Have you had a look at the Bioconductor documentation for this package:

http://bioconductor.org/packages/2.6/bioc/html/tigre.html

The 'tigre User Guide' describes the process of loading from affy data in section 3.2 and section 4 talks briefly about non-Affy data. The 'Reference Manual' describes the objects in detail, so should be easier than trying re-engineer what is happening from examining the R objects. Specifically, the ExpressionTimeSeries object you are examining appears to be an output of processing Affy data as opposed to an input.

For using this package on your organism instead of Drosophila, section 3.3 looks like the right place to start. It appears you will need mappings of your probes to genes. The getAnnMap function and annotation library look like the places to go to learn more.

Hope this helps. I've never used tigre before so can't offer any specific advice, but this is my general approach to learning a new Bioconductor package.

[Zhongshan]

Your suggestion is really good, thanks very much, and I will have a try.

Answer 5

[Zhongshan]

Thanks.

After using the str(drosophila_gpsim_fragment), I got the following results, but unfortunately, I don’t know how to print some of the data in the object. Actually, I am not good at R programming. I only know some basic skills. There are huge challenges for me to solve this problem, for example, I don’t understand this symbol .. .. ..@ data, which remind me that it looks like perl reference, and I try to use drosophila_gpsim_fragment@data to get some result, but with failure.

Another thing is that if I want to construct this kind of object in R, what should I do, is there some books I can read and get some clues from it?

Would you please show me how to print data in some of the objects? Thanks.

Formal class 'ExpressionTimeSeries' [package "tiger"] with 7 slots
  ..@ assayData        :<environment: 0x0263fb50> 
  ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':     3 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr [1:3] "time.h" "experiment ID" "modeltimes"
  .. .. ..@ data             :'data.frame':     36 obs. of  3 variables:
  .. .. .. ..$ time.h     : int [1:36] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. ..$ experiments: int [1:36] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ modeltime  : int [1:36] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ featureData      :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':     0 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr(0) 
  .. .. ..@ data             :'data.frame':     4 obs. of  0 variables
  .. .. ..@ dimLabels        : chr [1:2] "featureNames" "featureColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ experimentData   :Formal class 'MIAME' [package "Biobase"] with 13 slots
  .. .. ..@ name             : chr ""
  .. .. ..@ lab              : chr ""
  .. .. ..@ contact          : chr ""
  .. .. ..@ title            : chr ""
  .. .. ..@ abstract         : chr ""
  .. .. ..@ url              : chr ""
  .. .. ..@ pubMedIds        : chr ""
  .. .. ..@ samples          : list()
  .. .. ..@ hybridizations   : list()
  .. .. ..@ normControls     : list()
  .. .. ..@ preprocessing    :List of 2
  .. .. .. ..$ filenames  : chr [1:36] "/home/ahonkela/data/dros_data/embryo_tc_array_data/embryo_tc_4_1.CEL" "/home/ahonkela/data/dros_data/embryo_tc_array_data/embryo_tc_4_2.CEL" "/home/ahonkela/data/dros_data/embryo_tc_array_data/embryo_tc_4_3.CEL" "/home/ahonkela/data/dros_data/embryo_tc_array_data/embryo_tc_4_4.CEL" ...
  .. .. .. ..$ affyversion: chr NA
  .. .. ..@ other            :List of 1

[David W]

Hi zhongshan, I don't not anything about Tigre but the '@'s are "slots" within R classes. Type ?slot and ?Classes to get an idea of how they work