Vector

# with the concatenation function c()
vector.c <- c(1, 2, 3, 4, 5) 
vector.c
## [1] 1 2 3 4 5
animals <- c("cat", "sheep", "dog")
animals
## [1] "cat"   "sheep" "dog"
# with the sequence notation
vector.s <- 1:5
vector.s
## [1] 1 2 3 4 5
# with the rep() function
vector.r <- rep(1,5)
vector.r
## [1] 1 1 1 1 1


List

n = c(2, 3, 5) 
s = c("aa", "bb", "cc", "dd", "ee") 
b = c(TRUE, FALSE, TRUE, FALSE, FALSE) 
x = list(n, s, b, 3)   # x contains copies of n, s, b 
x
## [[1]]
## [1] 2 3 5
## 
## [[2]]
## [1] "aa" "bb" "cc" "dd" "ee"
## 
## [[3]]
## [1]  TRUE FALSE  TRUE FALSE FALSE
## 
## [[4]]
## [1] 3
x[[1]]
## [1] 2 3 5
y = list()
y[["one"]] =  c(2, 3, 5)
y[["two"]] = c("aa", "bb", "cc", "dd", "ee") 
y[["drei"]] = c(TRUE, FALSE, TRUE, FALSE, FALSE) 
y
## $one
## [1] 2 3 5
## 
## $two
## [1] "aa" "bb" "cc" "dd" "ee"
## 
## $drei
## [1]  TRUE FALSE  TRUE FALSE FALSE
y[["two"]]
## [1] "aa" "bb" "cc" "dd" "ee"


Matrix

mat = matrix(1:12, ncol=3)
mat
##      [,1] [,2] [,3]
## [1,]    1    5    9
## [2,]    2    6   10
## [3,]    3    7   11
## [4,]    4    8   12
mat2 <- matrix(letters[1:12], ncol=3, byrow=TRUE)
mat2
##      [,1] [,2] [,3]
## [1,] "a"  "b"  "c" 
## [2,] "d"  "e"  "f" 
## [3,] "g"  "h"  "i" 
## [4,] "j"  "k"  "l"
mat[1,]
## [1] 1 5 9
mat[,2:3]
##      [,1] [,2]
## [1,]    5    9
## [2,]    6   10
## [3,]    7   11
## [4,]    8   12


Array

arr <- array(1:24, dim=c(3,4,2))
arr
## , , 1
## 
##      [,1] [,2] [,3] [,4]
## [1,]    1    4    7   10
## [2,]    2    5    8   11
## [3,]    3    6    9   12
## 
## , , 2
## 
##      [,1] [,2] [,3] [,4]
## [1,]   13   16   19   22
## [2,]   14   17   20   23
## [3,]   15   18   21   24


Data frame

d <- c(1,2,3,4)
e <- c("red", "white", "red", NA)
f <- c(TRUE,TRUE,TRUE,FALSE)
mydata <- data.frame(ID = d, color = e, success = f)
mydata
##   ID color success
## 1  1   red    TRUE
## 2  2 white    TRUE
## 3  3   red    TRUE
## 4  4  <NA>   FALSE
mydata[1:2] 
##   ID color
## 1  1   red
## 2  2 white
## 3  3   red
## 4  4  <NA>
mydata[c("ID","color")]
##   ID color
## 1  1   red
## 2  2 white
## 3  3   red
## 4  4  <NA>
mydata$ID 
## [1] 1 2 3 4


Factor

gender <- c(rep("male",20), rep("female", 30))
gender <- factor(gender)
# stores gender as 20 1s and 30 2s and associates
# 1=female, 2=male internally (alphabetically)
summary(gender) 
## female   male 
##     30     20
levels(gender)
## [1] "female" "male"
as.character(gender)
##  [1] "male"   "male"   "male"   "male"   "male"   "male"   "male"  
##  [8] "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [15] "male"   "male"   "male"   "male"   "male"   "male"   "female"
## [22] "female" "female" "female" "female" "female" "female" "female"
## [29] "female" "female" "female" "female" "female" "female" "female"
## [36] "female" "female" "female" "female" "female" "female" "female"
## [43] "female" "female" "female" "female" "female" "female" "female"
## [50] "female"


Functions to explore objects

x <- matrix(1:25, ncol = 5)
colnames(x) = c("a", "b", "c", "d", "e")
rownames(x) = c("gene1", "gene2", "gene3", "gene4", "gene5")
x
##       a  b  c  d  e
## gene1 1  6 11 16 21
## gene2 2  7 12 17 22
## gene3 3  8 13 18 23
## gene4 4  9 14 19 24
## gene5 5 10 15 20 25
y = c(2, 4, 5, 2, 5, 7)
length(y)      # number of elements or components
## [1] 6
str(x)         # structure of an object
##  int [1:5, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : chr [1:5] "gene1" "gene2" "gene3" "gene4" ...
##   ..$ : chr [1:5] "a" "b" "c" "d" ...
class(x)       # class or type of an object
## [1] "matrix"
colnames(x)    # names
## [1] "a" "b" "c" "d" "e"
names(y)       # names
## NULL
ls()           # list current objects
##  [1] "aa_seqs"         "animals"         "arr"            
##  [4] "b"               "bio.tree"        "clouds"         
##  [7] "clres"           "colvec"          "condition1"     
## [10] "condition2"      "conditions"      "counts"         
## [13] "counts.selected" "cres"            "d"              
## [16] "de"              "design"          "detags"         
## [19] "df"              "dge"             "distance"       
## [22] "dna"             "dna2"            "dna3"           
## [25] "dna_seqs"        "e"               "et"             
## [28] "f"               "fastafile"       "gender"         
## [31] "InsectSprays"    "maintxt"         "mat"            
## [34] "mat2"            "mean.values"     "midpoints"      
## [37] "mydata"          "n"               "nr"             
## [40] "op"              "pinched_data"    "res"            
## [43] "s"               "sets"            "sets1"          
## [46] "stacked"         "std.dev"         "timedata"       
## [49] "tree.nj"         "tuk"             "vector.c"       
## [52] "vector.r"        "vector.s"        "x"              
## [55] "y"               "ylim"            "z"
rm(animals)    # delete an object
# newobject <- edit(x)  edit copy and save as newobject
# fix(x)                edit in place