R “Lists”

Introduction to R list data types: properties, how to create, and modify them and how to retrieve data.

Task…

Load the R-Exercise_BasicSetup project in RStudio if you don’t already have it open.
Type init() as instructed after the project has loaded.
Continue below.

Lists

The elements contained in matrices or arrays must all have the same type – character, numeric, logical or such. Data frames allow us to store elements of different types in columns, but all columns must have the same length and the elements have to be “atomic” - i.e. you can’t put vectors into dataframe columns. But R’s lists are much more versatile. They are simply ordered collections of components. These components can have different type - all kinds of R objects can go into a list: characters, booleans, any kind of numeric data, other lists, even functions - AND they can have different size.

Lists are created with the list() function, which works similar to the c() function for vectors. Components are accessed through their index in double square brackets, or through their name, using the “$” operator, if the name has been defined. Here is an example:

pUC19 <- list(size=2686, marker="ampicillin", ori="ColE1", accession="L01397", BanI=c(235, 408, 550, 1647) )

objectInfo(pUC19)
pUC19[[1]]
pUC19[[2]]
pUC19$ori
pUC19$BanI[2]

Note that in our data.frame() example, we stored multiple restriction enzymes in one string, separated by commas. While we can take such strings apart again, by using the strsplit() function, the string itself still has to be one single element in the data frame’s column. Lists have no such restriction. In our example above, we assigned a vector of restriction site positions to the element “BanI”.

You can easily imagine that we could now create a list of lists, and that list of lists could hold an entire plasmid database in a most versatile way. Let’s do this!

Task…

Create a list like the one above with data for pACYC184 following the structure for the pUC19 example but using only size, marker and ori data:

size: 4245

marker: Tet, Cam

ori: p15A
Confirm that your new list’s structure looks like the pUC19 one (minus “accession”, and the “BanI”” element).
Make a new list, call it plasmidDB and assign to it the puc19 list:

plasmidDB <- list()
plasmidDB[["pUC19"]] <- pUC19

Add your pACYC184 list
Add a third element to plasmidDB, “pBR322” using the pBR322 data:

size: 4361

marker: Amp, Tet

ori: ColE1
Then: retrieve the entire pACYC184 list.

Whereas data frames allow you to get all data from a column directly, this is not possible for lists. You need a function that iterates over all list elements instead. Such a function is lapply(), one of several “apply” functions. For example, to get all “ori” elements, try:

lapply(plasmidDB, function(x) { return(x$ori) })

Retrieve all sizes from the list. Use unlist() to flatten the result. Then use min() to find the size of the smallest one.

Lost? Solutions here (but don’t peek).

pUC19 <- list(size=2686, marker="ampicillin", ori="ColE1", accession="L01397", BanI=c(235, 408, 550, 1647) )
pACYC184 <- list(size=4245, marker="Tet, Cam", ori="p15A" )

plasmidDB <- list()
plasmidDB[["pUC19"]] <- pUC19
plasmidDB[["pACYC184"]] <- pACYC184
plasmidDB[["pBR322"]] <- list(size=4361, marker="Amp, Tet", ori="ColE1" )

plasmidDB[["pACYC184"]] # retrieve the entire pACYC184 list

lapply(plasmidDB, function(x) { return(x$ori) })
x <- unlist(lapply(plasmidDB, function(x) { return(x$size) }))
min(x)
# or, to get the name too ...
x[x == min(x)]

Practical tips:

How do I …

# Initialize an empty list?
#
# You need this if you want to pre-allocate a given number of empty
# slots into which you can place data later. In contrast to vectors, you
# can't just write to a non-existing slot of a list - the slot has to
# exist, although it may certainly be empty:

myList <- vector(mode = "list", length = 3)
myList
# [[1]]
# NULL
# 
# [[2]]
# NULL
# 
# [[3]]
# NULL

# Store or modify an element in a list?
#
myList[[2]]$xy <- c(1.4142, 1.618)
myList

# [[1]]
# NULL
# 
# [[2]]
# [[2]]$xy
# [1] 1.4142 1.6180
# 
# 
# [[3]]
# NULL

# Iterate over all elements of a list?
#
# Loop over the list length ...

for (i in seq_len(length(myList))) {
  print(myList[[i]]$xy)
}

# NULL
# [1] 1.4142 1.6180
# NULL

# Append an element to a list ...
# 
# Just use c(), and append an empty list or a list with values.
#
myList <- c(myList, NULL)                         # This does nothing!
myList <- c(myList, list(NULL))                   # This appends a new slot
myList[[length(myList)]]$myNeighbour <- "Totoro"  # This puts a named element
                                                  # into the last slot
myList

# [[1]]
# NULL
# 
# [[2]]
# [[2]]$xy
# [1] 1.4142 1.6180
# 
# 
# [[3]]
# NULL
# 
# [[4]]
# [[4]]$myNeighbour
# [1] "Totoro"

# Remove an elelment from a list?
#
# Just assign NULL to its slot ...

myList[[3]] <- NULL

myList


# [[1]]
# NULL
# 
# [[2]]
# [[2]]$xy
# [1] 1.4142 1.6180
# 
# 
# [[3]]
# [[3]]$myNeighbour
# [1] "Totoro"

Practice these steps from time to time until they feel natural.

Review

Question 1

Execute: x <- strsplit(plasmidData$Sites, ", ") and analyze the result.

What is plasmidData$Sites?
What is x?
Why does strsplit() have a list as return value, not a vector or a data frame?

Answer …

A vector of strings (character elements).
A list of vectors.
Because strsplit() is vectorized, i.e. it is able to operates on all elements of the vector plasmidData$Sites in one command. But the function doesn’t know in advance how many elements the result is going to have for each element. So it needs to output vectors of different lengths. And the only way to combine vectors of different length into a single value (note: all R functions return only a single value) is by collecting them in a list.

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