A few tricks on Matrices (1) The indices can still be give

1
An Introduction to R
Logic Basics
2
The R language

• Command line
• Can be executed within a terminal
• Within Emacs using ESS (Emacs Speaks Statistics)

3
Data structures

• Vector ( 1 dimensional array)
• gt vect c(4,6,7,10)
• gt vect2 c(vect,vect)
• Matrix ( 2 dimensional array)
• gt mat matrix(0, 2, 2) matrix of size 2x2,
  with 0
• gt mat matrix(vect, 2, 2) matrix of size 2x2
• Array ( n dimensional)
• gt array array(0, dimc(10,10,10)) cube of
  10x10x10

These data structures settle the R logic as all
is designed to make an easy use of it
4
A few tricks on Vectors

• The indices can be a vector ! Indices begin at
  1!!!
• gt vect.A c(4,6,7,10)
• gt vect.B c(1,4)
• gt vect.A1
• 4
• gt vect.Avect.B equivalent to
  vect.Ac(1,4)
• 4 10
• The WHICH() function is the most useful
• gt which(vect.A 7)3
• gt which(vect.A gt 6)
• 3 4
• The , seq and gl functions allow to
  generate sequence of numbers

5
A few tricks on Matrices (1)

• The indices can still be given as a vector !
• gt MY.matrixi,j give the element at line i,
  col j
• gt MY.matrixi, gives the line i
• gt MY.matrixc(1,2,3), gives the first 3 lines
  as a matrix
• gt MY.matrixc(1,2,3), c(1,2,3) gives a
  sub-matrix

j
i
i
6
A few tricks on Matrices (2)

• The WHICH() function is still very useful
• Prints extreme values of a matrix
• gt MY.matrixwhich(MY.matrix gt cutoff)here
  Values gt to cutoff are printed
• An example
• I have a file of the following type
• pdb NB_chains NB_identical_int
  NB_homologous_int NB_different_int
• gt data read.table(file /elevy/... )
• gt identical.1 which(data,3 1)
• gt dimers which(data,2 2)
• gt homodimers intersect(identical,dimers)
• gt datahomodimers, prints all the homodimer
  lines !

7
More tricks

• How many numbers in a matrix are equal to 5 ?
• How many numbers are in common between 2 matrices
  ?
• Replace all the 4 by -4 in any data structure ?

8
Some useful functions (1)

• Play with data structures
• min, max, which.min, which.max
• combined with sum
• mean, sd
• intersect
• cor combined with hclust / heatmap
• Cast operator as.type

9
Some useful functions (2)

• For text printing
• print(Hello)
• print(paste(one, i , two , j ,sep ))

10
Some useful functions (3)

• For statistical analysis
• rand / random doesnt exists ! Their are
  specific laws instead
• ? runif(x) Uniform law (equiv. To rand)
• ? rnorm(x) Gaussian law

11
Some useful functions (4)

• Useful graphical functions
• Plot 2D look at demo(graphics)
• Image 2D look at demo(image)
• Heatmap (clust image tree)
• par() store most of the graphical parameters to
  custom the display
• Persp 3D look at demo(persp)
• Find help examples
• help.start() or help(function) or ?function

12
Some remarks

• No  underscores  in variables names are allowed
• (the dot is generally used instead)
• The  dot  doesnt mean  method call  like in
  object oriented languages!
• There is actually another  vector like data
  structure list
• which allows to store objects rather than digits.
• There is actually another  matrix like  data
  structure data.frame which is a matrix for
  which rows/columns can be given a name

13
Last remarks

• You can run scripts in BATCH mode, example
• R --vanilla lt script.r
• To quit R, type q()
• The () are very important, when you dont put it
  the source code of the function is printed! (this
  is true for any function)
• Dont hesitate to ask questions ?