Data visualization
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@5640a555
Last seen 21 months ago
United States

Hi, This is a total Newbie question but could you please either have a repository of the data files you use in your examples or when putting up the tutorials give a few lines of what data you're using so that we can format our own data in the same way? I am super new to coding and so this is really helpful for me to understand the best way to bring my data into the system. For example I'm wanting to use your tutorial for Sequence Manipulation and Scanning and you have: data(ArabidopsisPromoters)

What does that look like? How should I format my data so I can follow along with the code using my own data? I've been scanning the website and haven't been able to find a file for it or a view of what the layout of that data should be.

Thank you so much! Jennifer

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
HELP Data • 593 views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 10 hours ago
Wageningen University, Wageningen, the …

A Google search learned me that you apparently are following the tutorial (vignette) for the package universalmotif. It would be helpful if you would have mentioned that in your post. Also, tagging your question with the package name universalmotif would (in principle) alert the maintainer of the package that you posted a question.

Anyway,the package universalmotif also contains some example data sets, including ArabidopsisPromoters.

After running library(universalmotif), you 'load' this dataset by data(ArabidopsisPromoters). Next you can check its class, contents, structure, etc. See below.

Please note that I have never used the package universalmotif myselves, so I cannot help you with that. If you have a question on how exactly to format your data for use with universalmotif, then I suggest you post a new question in which you show what type of data you have, the code you used to get it in R/Bioconductor, and what you would like to get ( a DNAStringSet apparently). Don't forget to add the tags universalmotif and Biostrings, and feel free to refer to this thread. The info on this page may get you started.

HTH, Guido

Based on the vignette:

> library(universalmotif)
> library(Biostrings)
> data(ArabidopsisPromoters)
> 
> ArabidopsisPromoters
DNAStringSet object of length 50:
     width seq                                           names               
 [1]  1000 CATACAAGTAACAGAAAAACC...CACTTTTGTCCGAAAACTAAG AT4G28150
 [2]  1000 TCGCTCATAGTTCTCCTAGAT...AATCCCAGTATTACCAACTTC AT1G19380
 [3]  1000 AATTGAAGGCTTTTACATCTT...TGAAAGTCTTCAAGCAGACGC AT4G19520
 [4]  1000 TCGTAAAGTTAAAGGGAGACG...TTAATAATCACATCTCTTACC AT1G03850
 [5]  1000 TACTTTTATGGATCATCATCA...GTGTAATGACGATGAAAGATG AT5G01810
 ...   ... ...
[46]  1000 ACAGCAAAAACTGAGGTGCGA...AGAGAGGACTGAGGAAATTCA AT5G22690
[47]  1000 GAATTGTGATACTATACTAAT...CCGTGCCCTTCATTTTCAGAA AT1G05670
[48]  1000 CATGCTTGGTTGGTTCTTCTT...AACTTAGTGCCACTTAGACAC AT1G06160
[49]  1000 AGTTTATTGAATTAAGTTTTT...AAGGAACGTTCAAGAACCAAA AT5G24660
[50]  1000 AGCGGTATATAAAAGTTAGTG...GGATGTTGATGCATGAAAATC AT3G19200
> 
> class(ArabidopsisPromoters)
[1] "DNAStringSet"
attr(,"package")
[1] "Biostrings"
> 
> str(ArabidopsisPromoters)
Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool           :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots
  .. .. ..@ xp_list                    :List of 1
  .. .. .. ..$ :<externalptr> 
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :<environment: 0x000001f274e327a0> 
  ..@ ranges         :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots
  .. .. ..@ group          : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..@ start          : int [1:50] 1 1001 2001 3001 4001 5001 6001 7001 8001 9001 ...
  .. .. ..@ width          : int [1:50] 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 ...
  .. .. ..@ NAMES          : chr [1:50] "AT4G28150" "AT1G19380" "AT4G19520" "AT1G03850" ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ elementType    : chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata       : list()
> 
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