Looking at Metadata

We are studying a population of Escherichia coli (designated Ara-3), which were propagated for more than 40,000 generations in a glucose-limited minimal medium. This medium was supplemented with citrate which E. coli cannot metabolize in the aerobic conditions of the experiment. Sequencing of the populations at regular time points reveals that spontaneous citrate-using mutants (Cit+) appeared at around 31,000 generations. This metadata describes information on the Ara-3 clones and the columns represent:

The metadata file required for this lesson can be downloaded directly here or viewed in Github.

Tip: If you can’t find the Ecoli_metadata.csv file, or have lost track of it, download the file directly using the R download.file() function

download.file("https://raw.githubusercontent.com/datacarpentry/R-genomics/gh-pages/data/Ecoli_metadata.csv", "data/Ecoli_metadata.csv")

You are now ready to load the data. We are going to use the R function read.csv() to load the data file into memory (as a data.frame):

metadata <- read.csv('data/Ecoli_metadata.csv')

This statement doesn’t produce any output because assignment doesn’t display anything. If we want to check that our data has been loaded, we can print the variable’s value.

metadata

This displays the whole dataset, which can be many rows! Instead, we can inspect just the first 6 rows of this data.frame using the function head():

head(metadata)

##     sample generation   clade strain     cit       run genome_size
## 1   REL606          0    <NA> REL606 unknown                  4.62
## 2 REL1166A       2000 unknown REL606 unknown SRR098028        4.63
## 3   ZDB409       5000 unknown REL606 unknown SRR098281        4.60
## 4   ZDB429      10000      UC REL606 unknown SRR098282        4.59
## 5   ZDB446      15000      UC REL606 unknown SRR098283        4.66
## 6   ZDB458      20000 (C1,C2) REL606 unknown SRR098284        4.63

We’ve just done two very useful things. 1. We’ve read our data in to R, so now we can work with it in R 2. We’ve created a data frame (with the read.csv command), the standard way R works with data.

What are data frames?

data.frame is the de facto data structure for most tabular data and what we use for statistics and plotting.

A data.frame is a collection of vectors of identical lengths. Each vector represents a column, and each vector can be of a different data type (e.g., characters, integers, factors). The str() function is useful to inspect the data types of the columns.

A data.frame can be created by the functions read.csv() or read.table(), in other words, when importing spreadsheets from your hard drive (or the web).

By default, data.frame converts (= coerces) columns that contain characters (i.e., text) into the factor data type. Depending on what you want to do with the data, you may want to keep these columns as character. To do so, read.csv() and read.table() have an argument called stringsAsFactors which can be set to FALSE.

Let’s now check the __str__ucture of this data.frame in more details with the function str():

str(metadata)

## 'data.frame':    30 obs. of  7 variables:
##  $ sample     : Factor w/ 30 levels "CZB152","CZB154",..: 7 6 18 19 20 21 22 23 24 25 ...
##  $ generation : int  0 2000 5000 10000 15000 20000 20000 20000 25000 25000 ...
##  $ clade      : Factor w/ 7 levels "(C1,C2)","C1",..: NA 7 7 6 6 1 1 1 2 4 ...
##  $ strain     : Factor w/ 1 level "REL606": 1 1 1 1 1 1 1 1 1 1 ...
##  $ cit        : Factor w/ 3 levels "minus","plus",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ run        : Factor w/ 30 levels "","SRR097977",..: 1 5 22 23 24 25 26 27 28 29 ...
##  $ genome_size: num  4.62 4.63 4.6 4.59 4.66 4.63 4.62 4.61 4.65 4.59 ...

Inspecting data.frame objects

We already saw how the functions head() and str() can be useful to check the content and the structure of a data.frame. Here is a non-exhaustive list of functions to get a sense of the content/structure of the data.

• Size:
  • dim() - returns a vector with the number of rows in the first element, and the number of columns as the second element (the __dim__ensions of the object)
  • nrow() - returns the number of rows
  • ncol() - returns the number of columns
• Content:
  • head() - shows the first 6 rows
  • tail() - shows the last 6 rows
• Names:
  • names() - returns the column names (synonym of colnames() for data.frame objects)
  • rownames() - returns the row names
• Summary:
  • str() - structure of the object and information about the class, length and content of each column
  • summary() - summary statistics for each column

Note: most of these functions are “generic”, they can be used on other types of objects besides data.frame.

Challenge

Using these functions, can you answer the following questions? * What is the class of the object metadata? * How many rows and how many columns are in this object? * How many citrate+ mutants have been recorded in this population?

As you can see, many of the columns in our data frame are of a special class called factor. Before we learn more about the data.frame class, we are going to talk about factors. They are very useful but not necessarily intuitive, and therefore require some attention.

str(metadata)

## 'data.frame':    30 obs. of  7 variables:
##  $ sample     : Factor w/ 30 levels "CZB152","CZB154",..: 7 6 18 19 20 21 22 23 24 25 ...
##  $ generation : int  0 2000 5000 10000 15000 20000 20000 20000 25000 25000 ...
##  $ clade      : Factor w/ 7 levels "(C1,C2)","C1",..: NA 7 7 6 6 1 1 1 2 4 ...
##  $ strain     : Factor w/ 1 level "REL606": 1 1 1 1 1 1 1 1 1 1 ...
##  $ cit        : Factor w/ 3 levels "minus","plus",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ run        : Factor w/ 30 levels "","SRR097977",..: 1 5 22 23 24 25 26 27 28 29 ...
##  $ genome_size: num  4.62 4.63 4.6 4.59 4.66 4.63 4.62 4.61 4.65 4.59 ...