Itmat pcbi-r-course-1
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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.

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 Itmat pcbi-r-course-1 Presentation Transcript

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