Difference between revisions of "RPR-Data-Import"

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Importing data in R
 
Importing data in R
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#f2fafa; font-size:30%; font-weight:200; color: #000000; ">
 
(Data import from unstructured text, structured text, spreadsheets, online repositories, and Web pages)
 
(Data import from unstructured text, structured text, spreadsheets, online repositories, and Web pages)
 
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<b>Abstract:</b><br />
 
<b>Abstract:</b><br />
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<b>Deliverables:</b><br />
 
<b>Deliverables:</b><br />
 
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
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*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
 
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=== Evaluation ===
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
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* Line endings
 
* Line endings
 
* Unstructured text files, headers, skip, omit, and rownames
 
* Unstructured text files, headers, skip, omit, and rownames
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* XML - libraries and cpath
 
* XML - libraries and cpath
 
* Binary Data
 
* Binary Data
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* R objects: save() and load()
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* text objects: readLines() and writeLines()
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* R objects: save() and load(); saveRDS() and readRDS().
  
  
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== Notes ==
 
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== Further reading, links and resources ==
 
== Further reading, links and resources ==
 
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<div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div>
 
<div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div>
 
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== Notes ==
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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*0.1 First stub
 
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Latest revision as of 01:41, 23 September 2020

Importing data in R

(Data import from unstructured text, structured text, spreadsheets, online repositories, and Web pages)


 


Abstract:

Practical for data import from text files, spreadsheets and Web pages.

Objectives:
...

Outcomes:
...

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:


     


    This page is not currently being maintained since it is not part of active learning sections.


     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    • Line endings
    • Unstructured text files, headers, skip, omit, and rownames
    • Caution with stringsAsFactors
    • Caution with coerced data
    • Text files with keywords
    • Text-files: changing state
    • Text-files: csv and tsv (and Excel sheets)
    • Text-files: slurping, chunking and streaming
    • curl
    • httr GET and POST
    • XML - libraries and cpath
    • Binary Data
    • text objects: readLines() and writeLines()
    • R objects: save() and load(); saveRDS() and readRDS().


    Regex for screenscraping example:

    Screenscraping

    Write a PHP program that screenscrapes resolution data for a protein structure file from the PDB. 

     Here is a link to a PDB record to illustrate the URL format.

       Fetch the contents of the URL into a string. Use a regex that captures the data you want to retrieve as part of some unique pattern in the HTML source. Print.

       ;The regex:
    :/\s*(\d+\.\d+)/ *   identifying tag for the information we are looking for, ... 
       *\s*   ... probably followed by whitespace, ...
   *(\d+\.\d+)   ... the "payload" of the match: one or more digits, a literal dot and and one or more digits.

       ;The code:
   <source lang="PHP">
   <?php
 $URLpath = "http://www.pdb.org/pdb/explore/explore.do?structureId=";
 $PDBid = "2imm";
 $source = file_get_contents($URLpath . $PDBid);
    preg_match('/\s*?(\d+\.\d+)/', $source, $resolution); 
     print($resolution[1]);
 ?>




    Self-evaluation

    Further reading, links and resources

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-09-17

    Modified:

    2018-01-31

    Version:

    1.0

    Version history:

    • 1.0 first live version
    • 0.2 Contents outline
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    This page is not currently being maintained since it is not part of active learning sections.
    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=RPR-Data-Import&oldid=11595"