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    R Programming: © 2016 SMART Training Resources Pvt. LTD

    Uploaded by

    Srinivasan Krishnan

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    © All Rights Reserved
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    R Programming: © 2016 SMART Training Resources Pvt. LTD

    Uploaded by

    Srinivasan Krishnan
    28 views28 pages

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    28 views28 pages

    R Programming: © 2016 SMART Training Resources Pvt. LTD

    Uploaded by

    Srinivasan Krishnan

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
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    R Programming

    © 2016 SMART Training Resources Pvt. Ltd.


    Overview

    1. The Basics

    2. R Data Structures

    3. Data Input/Output

    4. In-Built Functions

    5. Data Visualization
    What R does and does not
    • data handling and storage: • is not a database, but
    numeric, textual connects to DBMSs

    • matrix algebra • has no graphical user


    interfaces, but connects to
    • hash tables and regular Java, TclTk
    expressions
    • language interpreter can be
    • high-level data analytic very slow, but allows to
    and statistical functions call own C/C++ code
    • classes (“OO”) • no spreadsheet view of
    • graphics data, but connects to Excel
    • programming language: / MsOffice
    loops, branching, • no professional /
    subroutines commercial support
    R and statistics
    • Packaging: a crucial infrastructure to efficiently
    produce, load and keep consistent software libraries
    from (many) different sources / authors
    • Statistics: most packages deal with statistics and data
    analysis
    • State of the art: many statistical researchers provide
    their methods as R packages
    > 1550+2000
    R as a Calculator
    [1] 3550
    or various calculations in the same row

    1.0
    > 2+3; 5*9; 6-6
    [1] 5
    [1] 45

    0.5
    sin(seq(0, 2 * pi, length = 100))
    [1] 0

    0.0
    > log2(32)

    [1] 5

    -0.5
    > sqrt(2)

    [1] 1.414214
    -1.0

    > seq(0, 5, length=6)


    0 20 40 60 80 100

    Index
    [1] 0 1 2 3 4 5
    > plot(sin(seq(0, 2*pi, length=100)))
    Variables
    > i = 81
    > sqrt(i) numeric
    [1] 9

    > prov = "All that Glitters are not Gold"


    character
    > sub("Glitters ","Glisters",prov)
    [1] " All that Glisters are not Gold“ string

    > 1>2
    [1] FALSE logical
    Object orientation
    primitive (or: atomic) data types in R are:

    • numeric (integer, double, complex)


    • character
    • logical
    • function
    Numbers in R: NAN and NA

    • NAN (not a number)


    • NA (missing value)
    o Basic handling of missing values
    >x
    [1] 1 2 3 4 5 6 7 8 NA
    > mean(x)
    [1] NA
    > mean(x,na.rm=TRUE)
    [1] 4.5
    Objects in R

    • Objects in R obtain values by assignment.


    • This is achieved by the gets arrow, <-, and not the
    equal sign, =.
    • Objects can be of different kinds.
    R Data Structures

    Vector
    Matrix
    Array
    Factor
    Data Frame
    List
    Vectors
    • vector: an ordered collection of data of the same type

    > a = c(1,2,3)
    > a*2
    [1] 2 4 6

    • In R, a single number is the special case of a vector with 1


    element.
    • Other vector types: character strings, logical
    Vectors
    • Create a vector
    > x <- 1:10
    • Give the elements some names
    > names(x) <-
    c("first","second","third","fourth","fifth")

    • Select elements based on another vector


    > i <- c(1,5)
    > x[i]
    first fifth
    1 5
    > x[-c(i,8)]
    second third fourth <NA> <NA> <NA> <NA>
    2 3 4 6 7 9 10
    Matrices

    • matrix: a rectangular table of data of the same type

    • array: 3-,4-,..dimensional matrix


    • example: the red and green foreground and background
    values for 20000 spots on 120 chips: a 4 x 20000 x 120 (3D)
    array.
    Matrices
    • Create an array
    > x <- array(1:10, dim = c(2, 5))
    >x
    [,1] [,2] [,3] [,4] [,5]
    [1,] 1 3 5 7 9
    [2,] 2 4 6 8 10
    > attributes(x)
    $dim
    [1] 2 5
    > dim(x)
    [1] 2 5
    Matrices
    • Set column or row names
    > colnames(x) <- c("col1", "col2", "col3", "col4", "5", "6")
    >x
    col1 col2 col3 col4 col5
    [1,] 1 3 5 7 9
    [2,] 2 4 6 8 10
    > colnames(x)[1] <- "column1"
    >x
    column1 col2 col3 col4 col5
    [1,] 1 3 5 7 9
    [2,] 2 4 6 8 10
    Matrix
    • Set row and columns names using dimnames
    > dimnames(x) <- list(c("first", "second"), NULL)
    >x
    column1 col2 col3 col4 col5
    first 1 3 5 7 9
    second 2 4 6 8 10
    • Setting dimension names
    > dimnames(x) <- list(my.rows = c("first", "second"), my.cols = NULL)
    >x
    my.cols
    my.rows [,1] [,2] [,3] [,4] [,5]
    first 1 3 5 7 9
    second 2 4 6 8 10
    Lists
    • vector: an ordered collection of data of the same type.
    > a = c(7,5,1)
    > a[2]
    [1] 5
    • list: an ordered collection of data of arbitrary types.
    > doe = list(name="john",age=28,married=F)
    > doe$name
    [1] "john“
    > doe$age
    [1] 28
    • Typically, vector elements are accessed by their index (an integer),
    list elements by their name (a character string). But both types
    support both access methods.
    Data frames
    • data frame: is supposed to represent the typical data table that
    researchers come up with – like a spreadsheet.

    • It is a rectangular table with rows and columns; data within


    each column has the same type (e.g. number, text, logical), but
    different columns may have different types.

    Example:
    >a
    localisation tumorsize progress
    XX348 proximal 6.3 FALSE
    XX234 distal 8.0 TRUE
    XX987 proximal 10.0 FALSE
    Factors
    • A character string can contain arbitrary text. Sometimes it is useful
    to use a limited vocabulary, with a small number of allowed
    words. A factor is a variable that can only take such a limited
    number of values, which are called levels.
    • Example
    • a family of two girls (1) and four boys(0),
    >kids = factor(c(1,0,1,0,0,0),levels=c(0,1),
    labels=c("boy","girl"))
    > Kids
    [1] girl boy girl boy boy boy
    Levels: boy girl
    > class(kids)
    [1] "factor"
    Data Input/Output
    Directory management
    • dir() list files in directory
    • setwd(path) set working directory
    • getwd() get working directory
    • ?files File and Directory Manipulation

    Standard ASCII Format


    • read.csv read comma-delimited file
    • write.csv write comma-delimited file
    Reading

    > sets <- read.csv("Sets_All.csv", header = TRUE)


    > sets$Ordered.Year <- ordered(sets$Year)
    > sets$SpotCd.Fac <- factor(sets$SpotCd, exclude = NULL)
    > spotted.sets <- sets[sets$Sp1Cd == 2, ]

    > write.csv(spotted.sets, file = "spotted.txt", row.names =


    FALSE)
    Data Visualization

    • plot() is the main graphing function


    • Automatically produces simple plots for vectors, functions or data
    frames
    Sample Data Set
    Plotting a Vector

    • plot(v) will print the elements of the vector v according to their


    index
    # Plot height for each observation
    > plot(dataset$Height)
    # Plot values against their ranks
    > plot(sort(dataset$Height))
    Common Parameters for
    plot()
    • Specifying labels:
    o main: provides a title
    o xlab: label for the x axis
    o Ylab: label for the y axis
    • Specifying range limits
    o ylim – 2-element vector gives range for x axis
    o xlim – 2-element vector gives range for y axis
    • Example

    o plot(sort(dataset$Height), ylim = c(120,200), ylab =


    "Height (in cm)", xlab = "Rank", main = "Distribution of
    Heights”)
    Plotting Two Vectors

    • plot()can pair elements from 2 vectors to produce x-y coordinates


    • plot() and pairs() can also produce composite plots that pair all the
    variables in a data frame.
    • Example
    o plot(dataset$Hip, dataset$Waist, xlab = "Hip", ylab = "Waist", main =
    "Circumference (in cm)", pch = 2, col = "blue")
    Histograms

    • Generated by the hist() function


    • The parameter breaks is key
    o Specifies the number of categories to plot
    or
    o Specifies the breakpoints for each category
    • The xlab, ylab, xlim, ylim options work as expected
    • Example
    o hist(dataset$bp.sys, col = "lightblue", xlab = "Systolic Blood Pressure",
    main = "Blood Pressure“)
    End of Session
    Thank you…

    © 2016 SMART Training Resources Pvt. Ltd.

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