R Tutorial

How to list files in a directory/folder?> list.files("~/Documents/linuxDatPro") [1] "chrs_2L_snps.csv~" "chrs_all_snps.csv~" "dgrp" [4] "linux_data_manipulation.odt" "perl_scripts.odt" "regexp.pdf" [7] "sed1line.txt" "shell_script" "story.txt" [10] "story.txt~" "userlogin.sh~" "while01.awk~"

Data types1. Numeric2. Integer3. Complex4. Logical5. Character6. Vector7. Matrix8. List9. Dataframe

NumericIt is the default computational data type.

Decimals Integers

To find out, use: class()

> x class(x)[1] "numeric"

> y class(y)[1] "numeric"> is.integer(y)[1] FALSE

IntegerIn order to create an integer variable in R, we invoke:

as.integer()

> k k

[1] 10> class(k)[1] "integer"

Coerce a decimal as integer. Use: as.integer()

To find out, use: is.integer()

> j j[1] 2> class(j)[1] "integer"> is.integer(j)[1] TRUE

Integers and logical valuesOften, it is useful to perform arithmetic on logical values. Like the C language, TRUE has the value 1, while FALSE has value 0. > as.integer(TRUE)[1] 1> as.integer(FALSE)[1] 0

Complex> z z[1] 1+2i> class(z)[1] "complex"

Logical> j m x> m[1] FALSE> class(m)[1] "logical"

Standard logical operations are "&" (and), "|" (or), and "!" (negation). > a b a & b[1] FALSE> a | b[1] TRUE> !a[1] FALSE

Character: creation, concatenationCreate character string with:

quotesTo concatenate, use:

paste()

> fname lname fullName fullName[1] "Mahesh Vaishnav"> class(fname)[1] "character"> class(lname)[1] "character"> class(fullName)[1] "character"

Character: sprintf()However, it is often more convenient to create a readable string with the sprintf function, which has a Clanguage syntax. > sprintf("%s has %d dollars.", "Joe", 500)[1] "Joe has 500 dollars."

Character: substr()To extract a substring, we apply the substr function. Here is an example showing how to extract the substring between the second and twelfth positions in a string.> substr("Joe has 500 dollars.", start=2, stop=12)[1] "oe has 500 "

Character: sub()And to replace the first occurrence of the word "little" by another word "big" in the string, we apply thesub function.> sub("500", "1000", "Joe has 500 dollars.")[1] "Joe has 1000 dollars."

Membership: Testing and coercion Membership relates to the class of an object. Asks: is.something Coercion changes the class of an object. Says: as.something

See p31, Crawley, for Testing and Coercing functions.

Logical variable coerced to factors and numericsCreate a logical variable:

> lv lv[1] TRUE FALSE TRUE

Assess its membership using is.logical() function.> is.logical(lv)[1] TRUE

It is not a factor, so does not have levels:> levels(lv)NULL

But we can coerce it to a two-factor level, because it does have 2 levels, TRUE and FALSE:> fv fv[1] TRUE FALSE TRUE Levels: FALSE TRUE> is.factor(fv)[1] TRUE

We can coerce it to be a numeric variable too: TRUE evaluates to 1 FALSE evaluates to 0

> nv nv[1] 1 0 1> is.numeric(nv)[1] TRUE

Significance: useful as a shortcut when creating new factors with reduced number of levels, as we do in

model simplification.

Factor levels coerced into numerics> char char[1] "a" "b" "c"> class(char)[1] "character"> as.numeric(factor(char))[1] 1 2 3> as.numeric(char)[1] NA NA NAWarning message:NAs introduced by coercion

However,> as.numeric(c("a", "4", "c"))[1] NA 4 NAWarning message:NAs introduced by coercion

Here: character 4 was coerced into being a number, but a and c could not.