Intro to using R for Bioinformatics: Part 1 : The Basics<br />Angel Pizarro<br />angel@upenn.edu<br />
Injecting a bit of reality<br />
Taking it a bit further…<br />Waxing floors is not fun, and may not seem relevant, but have some faith Daniel-san<br />
Outline<br />We will teach you some basic uses of R<br />“Do & Tell” method where you will be asked to do an exercise and ...
What is        ?<br />R is a language and environment for statistical computing and graphics. <br />– http://www.r-project...
Install & Run R<br />You should have already installed R, but if you had trouble please see us after class <br />Start R<b...
Help is plentiful<br />Help in three ways<br />Too much! Get me out!<br />
More Help<br />help.start()<br />Start an HTML help session<br />help(mean)<br />Looks up the mean() function's help page<...
Whet your appetite…<br />
The Basics<br />Please enter each of the following lines into your R session:<br />
Basic Algebra<br />You will also see this form:<br />
Variables<br />“x” and “y” are variables. <br />They are pointers to some value<br />They can also be pointers to some fun...
Vectors<br />Enter this in your session:<br />Results<br />
Small tangent: What is “c (1,2,3)”?<br />Use  the help()<br />
Accessing Vector Members<br />In R, Vectors start indexes at 1. Most programming languages start indexing at zero<br />Als...
Small Tangent 2: Creating Sequences<br />Create regular sequences using a colon<br />Colon has high operator precedence<br...
Vectors<br />Are a list of  items of the same data type<br />Short for “double precision floating point number”<br />
Doing Stuff with Vectors<br />Math operations occur on each element in sequence<br />Returns a vector of the same size <br />
Factors<br />Simply a vector of items that mean something<br />Disease classifications, drug dosage, US states, months, ha...
Array and Matrix<br />Multi-dimensional generalizations of vectors<br />k-dimensions where k > 0<br />Assigned by the dim ...
Example<br />An INDEX ARRAY<br />
List<br />An ordered collection of named components<br />
List Access<br />
Data Frame<br />Bastard step child of List and Matrix<br />Essentially a list of vectors of same length<br />Closest repre...
Functions<br />We’ve already used them<br />Functions take in arguments and perform some action using those arguments. <br...
Example<br />
Write to CSV file<br />Extra column of the row indices<br />
Save your work!<br />R keeps track of your data and functions<br />You can start from where you left off if you save these...
Start from your save point<br />
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Itmat pcbi-r-course-1

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First part of 3-part course on teaching the R statistical package.

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  • Exercise 1: Use the sequence function to 1:20 by 2Exercise 2: Use rep() to create a vector with a sequence of number from 1 to 3, repeated three timesExercise 3: Create a vector 1:10 with 3 consecutive repeating values (e.g. 1 1 1 2 2 2 … 10 10 10 )
  • Changing the data type of a single element changes the type of the rest of the elements.The one exception to this is “missing values” represented by the special constant “NA”. See example above
  • Itmat pcbi-r-course-1

    1. 1. Intro to using R for Bioinformatics: Part 1 : The Basics<br />Angel Pizarro<br />angel@upenn.edu<br />
    2. 2. Injecting a bit of reality<br />
    3. 3. Taking it a bit further…<br />Waxing floors is not fun, and may not seem relevant, but have some faith Daniel-san<br />
    4. 4. Outline<br />We will teach you some basic uses of R<br />“Do & Tell” method where you will be asked to do an exercise and once done, we will explain what just happened.<br />Will cover basics, plotting and microarray analysis<br />We will not teach you statistics.<br />
    5. 5. What is ?<br />R is a language and environment for statistical computing and graphics. <br />– http://www.r-project.org <br />You can do stuff like this<br />
    6. 6. Install & Run R<br />You should have already installed R, but if you had trouble please see us after class <br />Start R<br />On Windows, use Tinn-R<br />On Mac, use the source R application<br />On Linux, use the console<br />
    7. 7. Help is plentiful<br />Help in three ways<br />Too much! Get me out!<br />
    8. 8. More Help<br />help.start()<br />Start an HTML help session<br />help(mean)<br />Looks up the mean() function's help page<br />?mean <br />help.search(mean) <br />Displays all help pages that contain text “mean”<br />??mean <br />
    9. 9. Whet your appetite…<br />
    10. 10. The Basics<br />Please enter each of the following lines into your R session:<br />
    11. 11.
    12. 12.
    13. 13.
    14. 14. Basic Algebra<br />You will also see this form:<br />
    15. 15. Variables<br />“x” and “y” are variables. <br />They are pointers to some value<br />They can also be pointers to some function<br />
    16. 16. Vectors<br />Enter this in your session:<br />Results<br />
    17. 17. Small tangent: What is “c (1,2,3)”?<br />Use the help()<br />
    18. 18. Accessing Vector Members<br />In R, Vectors start indexes at 1. Most programming languages start indexing at zero<br />Also, NOT WHAT YOU THINK IT IS! It is a INDEX VECTOR, meaning that you access the members of a vector with a vector<br />
    19. 19. Small Tangent 2: Creating Sequences<br />Create regular sequences using a colon<br />Colon has high operator precedence<br />Also see the seq() function<br />
    20. 20. Vectors<br />Are a list of items of the same data type<br />Short for “double precision floating point number”<br />
    21. 21. Doing Stuff with Vectors<br />Math operations occur on each element in sequence<br />Returns a vector of the same size <br />
    22. 22. Factors<br />Simply a vector of items that mean something<br />Disease classifications, drug dosage, US states, months, hapmap ethnic group<br />Can be ordered<br />Can have multiple levels<br />GO Functions<br />
    23. 23. Array and Matrix<br />Multi-dimensional generalizations of vectors<br />k-dimensions where k > 0<br />Assigned by the dim attribute<br />Can be indexed by two or more indices<br />If a single index value (can be a vector) is given, then dim is ignored and underlying vector values are accessed directly<br />Unless the given index values is also an array<br />Matrix is a two-dimensional array<br />
    24. 24. Example<br />An INDEX ARRAY<br />
    25. 25. List<br />An ordered collection of named components<br />
    26. 26. List Access<br />
    27. 27. Data Frame<br />Bastard step child of List and Matrix<br />Essentially a list of vectors of same length<br />Closest representation to an Excel file in R<br />Easiest way to make one is to read in a CSV file<br />
    28. 28.
    29. 29.
    30. 30. Functions<br />We’ve already used them<br />Functions take in arguments and perform some action using those arguments. <br />Actions do not affect the input arguments<br />
    31. 31. Example<br />
    32. 32. Write to CSV file<br />Extra column of the row indices<br />
    33. 33. Save your work!<br />R keeps track of your data and functions<br />You can start from where you left off if you save these to some file<br />
    34. 34. Start from your save point<br />
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