R Data Skills for Bioinformatics

Data Import

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Overview

Teaching: 20 min
Exercises: 10 min

Questions

How to read data in R?

What are some potential problems with reading data in R?

How to write data in files?

Objectives

To understand how to read data into R

To learn most commonly used functions in readr for reading the files

To understand and be able to fix common problems in reading data files

To know how to write data into a file

Data import

Introduction

Before transforming data we have to learn how to read them into R. We’ll start by learning how to read plain-text rectangular files into R. We’ll finish with a few pointers to packages that are useful for other types of data.

The tutorial is based on Chapter 10 of the R for Data Science book by Garrett Grolemund and Hadley Wickham. Check this book for more details.

Prerequisites

We’ll be using package readr to load flat files into R. This packages is a part of the core tidyverse, an “an opinionated collection of R packages designed for data science”.

if (!require("tidyverse")) install.packages("tidyverse")
library(tidyverse)

Getting started

The four most commonly used functions in readr are read_csv, read_csv2, read_tsv, and read_delim.

read_csv() reads comma delimited files,
read_csv2() reads semicolon separated files (common in countries where , is used as the decimal place),
read_tsv() reads tab delimited files, and
read_delim() reads in files with any delimiter.

These functions all have similar syntax; we will use read_csv as an example.

The first argument to read_csv() is the to the file to read.

heights <- read_csv("../data/heights.csv")

Parsed with column specification:
cols(
  earn = col_double(),
  height = col_double(),
  sex = col_character(),
  ed = col_integer(),
  age = col_integer(),
  race = col_character()
)

When you run read_csv() it prints out a column specification that gives the name and type of each column.

You can also supply an inline csv file. This is useful for experimenting with readr and for creating reproducible examples to share with others:

read_csv("a,b,c
1,2,3
4,5,6")

# A tibble: 2 x 3
      a     b     c
  <int> <int> <int>
1     1     2     3
2     4     5     6

In both cases read_csv() uses the first line of the data for the column names, which is a very common convention. There are two cases where you might want to tweak this behaviour:

Sometimes there are a few lines of metadata at the top of the file. You can use skip = n to skip the first n lines; or use comment = "#" to drop all lines that start with (e.g.) #.

read_csv("The first line of metadata
  The second line of metadata
  x,y,z
  1,2,3", skip = 2)

# A tibble: 1 x 3
      x     y     z
  <int> <int> <int>
1     1     2     3

read_csv("# A comment I want to skip
  x,y,z
  1,2,3", comment = "#")

# A tibble: 1 x 3
      x     y     z
  <int> <int> <int>
1     1     2     3

The data might not have column names. You can use col_names = FALSE to tell read_csv() not to treat the first row as headings, and instead label them sequentially from X1 to Xn. Alternatively you can pass col_names a character vector which will be used as the column names:
```
read_csv("1,2,3\n4,5,6", col_names = c("x", "y", "z"))
```
```
# A tibble: 2 x 3
      x     y     z
  <int> <int> <int>
1     1     2     3
2     4     5     6
```

Another option that commonly needs tweaking is na: this specifies the value (or values) that are used to represent missing values in your file:

read_csv("a,b,c\n1,2,.", na = ".")

# A tibble: 1 x 3
      a     b c    
  <int> <int> <chr>
1     1     2 <NA> 

Compared to base R

If you’ve used R before, you might wonder why we’re not using read.csv(). There are a few good reasons to favour readr functions over the base equivalents:

They are typically much faster (~10x) than their base equivalents. There is even a faster version, data.table::fread(), but it doesn’t fit quite so well into the tidyverse.
They produce tibbles, they don’t convert character vectors to factors, use row names, or munge the column names. These are common sources of frustration with the base R functions.
They are more reproducible. Base R functions inherit some behaviour from your operating system and environment variables, so import code that works on your computer might not work on someone else’s.

Writing to a file

readr also comes with two useful functions for writing data back to disk: write_csv() and write_tsv(). Both functions increase the chances of the output file being read back in correctly by:

Always encoding strings in UTF-8.
Saving dates and date-times in ISO8601 format so they are easily parsed elsewhere.

If you want to export a csv file to Excel, use write_excel_csv() — this writes a special character (a “byte order mark”) at the start of the file which tells Excel that you’re using the UTF-8 encoding.

The most important arguments are x (the data frame to save), and path (the location to save it). You can also specify how missing values are written with na, and if you want to append to an existing file.

write_csv(challenge, "challenge.csv")

Note that the type information is lost when you save to csv:

challenge

# A tibble: 2,000 x 2
       x y         
   <dbl> <date>    
 404 NA        
4172 NA        
3004 NA        
 787 NA        
  37 NA        
2332 NA        
2489 NA        
1449 NA        
3665 NA        
3863 NA        
# … with 1,990 more rows

write_csv(challenge, "challenge-2.csv")
read_csv("challenge-2.csv")

Parsed with column specification:
cols(
  x = col_integer(),
  y = col_character()
)

# A tibble: 2,000 x 2
       x y    
   <int> <chr>
 404 <NA> 
4172 <NA> 
3004 <NA> 
 787 <NA> 
  37 <NA> 
2332 <NA> 
2489 <NA> 
1449 <NA> 
3665 <NA> 
3863 <NA> 
# … with 1,990 more rows

This makes CSVs a little unreliable for caching interim results—you need to recreate the column specification every time you load in. There are two alternatives:

write_rds() and read_rds() are uniform wrappers around the base functions readRDS() and saveRDS(). These store data in R’s custom binary format called RDS:

write_rds(challenge, "challenge.rds")
read_rds("challenge.rds")

# A tibble: 2,000 x 2
       x y         
   <dbl> <date>    
 404 NA        
4172 NA        
3004 NA        
 787 NA        
  37 NA        
2332 NA        
2489 NA        
1449 NA        
3665 NA        
3863 NA        
# … with 1,990 more rows

The feather package implements a fast binary file format that can be shared across programming languages:

library(feather)
write_feather(challenge, "challenge.feather")
read_feather("challenge.feather")
#> # A tibble: 2,000 x 2
#>       x      y
#>   <dbl> <date>
#> 1   404   <NA>
#> 2  4172   <NA>
#> 3  3004   <NA>
#> 4   787   <NA>
#> 5    37   <NA>
#> 6  2332   <NA>
#> # ... with 1,994 more rows

Feather tends to be faster than RDS and is usable outside of R. However, RDS supports list-columns while feather currently does not.

Other types of data

To get other types of data into R, we recommend starting with the tidyverse packages listed below. They’re certainly not perfect, but they are a good place to start. For rectangular data:

haven reads SPSS, Stata, and SAS files.
readxl reads excel files (both .xls and .xlsx).
DBI, along with a database specific backend (e.g. RMySQL, RSQLite, RPostgreSQL etc) allows you to run SQL queries against a database and return a data frame.

For hierarchical data: use jsonlite (by Jeroen Ooms) for json, and xml2 for XML. Jenny Bryan has some excellent worked examples at https://jennybc.github.io/purrr-tutorial/.

For other file types, try the R data import/export manual and the rio package.

Homework

Parse the UNIX assignment files (fang_et_al_genotypes.txt and snp_position.txt) into R.

What problems did you encounter?

Did R guessed the data type correctly?

If not, how did you fix it?

Try to use the t function to transpose the first file

Did it work?

Can you figure out how to make it work?

Parsing a vector (read if you run into problems or if like details)

Before we get into the details of how readr reads files from disk, we need to take a little detour to talk about the parse_*() functions. These functions take a character vector and return a more specialised vector like a logical, integer, or date. These functions are useful in their own right, but are also an important building block for readr. Like all functions in the tidyverse, the parse_*() functions are uniform: the first argument is a character vector to parse, and the na argument specifies which strings should be treated as missing:

parse_integer(c("1", "231", ".", "456"), na = ".")

[1]   1 231  NA 456

If parsing fails, you’ll get a warning:

x <- parse_integer(c("123", "345", "abc", "123.45"))

Warning in rbind(names(probs), probs_f): number of columns of result is not
a multiple of vector length (arg 1)

Warning: 2 parsing failures.
row # A tibble: 2 x 4 col     row   col expected               actual expected   <int> <int> <chr>                  <chr>  actual 1     3    NA an integer             abc    row 2     4    NA no trailing characters .45   

And the failures will be missing in the output:

[1] 123 345  NA  NA
attr(,"problems")
# A tibble: 2 x 4
    row   col expected               actual
  <int> <int> <chr>                  <chr> 
1     3    NA an integer             abc   
2     4    NA no trailing characters .45   

There are severeal important parsers, but we will look just at two types:

number parsers: parse_double() is a strict numeric parser, and parse_number() is a flexible numeric parser.
character parser: parse_character().

The following sections describe these parsers in more detail.

Numbers

It seems like it should be straightforward to parse a number, but three problems make it tricky:

People write numbers differently in different parts of the world.
Numbers are often surrounded by other characters that provide some context, like “$1000” or “10%”.
Numbers often contain “grouping” characters to make them easier to read, like “1,000,000”, and these grouping characters vary around the world.

To address the first problem, readr has the notion of a “locale”, an object that specifies parsing options that differ from place to place. When parsing numbers, the most important option is the character you use for the decimal mark. You can override the default value of . by creating a new locale and setting the decimal_mark argument:

parse_double("1.23")

[1] 1.23

parse_double("1,23", locale = locale(decimal_mark = ","))

[1] 1.23

parse_number() addresses the second problem: it ignores non-numeric characters before and after the number. This is particularly useful for currencies and percentages, but also works to extract numbers embedded in text.

parse_number("$100")

[1] 100

parse_number("20%")

[1] 20

parse_number("It cost $123.45")

[1] 123.45

The final problem is addressed by the combination of parse_number() and the locale as parse_number() will ignore the “grouping mark”:

# Used in America
parse_number("$123,456,789")

[1] 123456789

# Used in many parts of Europe
parse_number("123.456.789", locale = locale(grouping_mark = "."))

[1] 123456789

# Used in Switzerland
parse_number("123'456'789", locale = locale(grouping_mark = "'"))

[1] 123456789

Strings

It seems like parse_character() should be really simple but it’s not, as there are multiple ways to represent the same string. To understand what’s going on, we need to dive into the details of how computers represent strings. In R, we can get at the underlying representation of a string using charToRaw():

charToRaw("Hadley")

[1] 48 61 64 6c 65 79

Each hexadecimal number represents a byte of information: 48 is H, 61 is a, and so on. The mapping from hexadecimal number to character is called the encoding, and in this case the encoding is called ASCII. ASCII does a great job of representing English characters, because it’s the American Standard Code for Information Interchange.

Things get more complicated for languages other than English as there are many competing standards for encoding non-English characters. Fortunately, today there is one standard that is supported almost everywhere: UTF-8. UTF-8 can encode just about every character used by humans today, as well as many extra symbols (like emoji!).

readr uses UTF-8 everywhere: it assumes your data is UTF-8 encoded when you read it, and always uses it when writing. This is a good default, but will fail for data produced by older systems that don’t understand UTF-8. If this happens to you, your strings will look weird when you print them. Sometimes just one or two characters might be messed up; other times you’ll get complete gibberish. For example:

x1 <- "El Ni\xf1o was particularly bad this year"
x2 <- "\x82\xb1\x82\xf1\x82\xc9\x82\xbf\x82\xcd"

x1

[1] "El Ni\xf1o was particularly bad this year"

x2

[1] "\x82\xb1\x82\xf1\x82\u0242\xbf\x82\xcd"

To fix the problem you need to specify the encoding in parse_character():

parse_character(x1, locale = locale(encoding = "Latin1"))

[1] "El Niño was particularly bad this year"

parse_character(x2, locale = locale(encoding = "Shift-JIS"))

[1] "こんにちは"

How do you find the correct encoding? If you’re lucky, it’ll be included somewhere in the data documentation. If not, readr provides guess_encoding() to help you figure it out. It’s not foolproof, and it works better when you have lots of text (unlike here), but it’s a reasonable place to start.

guess_encoding(charToRaw(x1))

# A tibble: 2 x 2
  encoding   confidence
  <chr>           <dbl>
1 ISO-8859-1       0.46
2 ISO-8859-9       0.23

guess_encoding(charToRaw(x2))

# A tibble: 1 x 2
  encoding confidence
  <chr>         <dbl>
1 KOI8-R         0.42

The first argument to guess_encoding() can either be a path to a file, or, as in this case, a raw vector (useful if the strings are already in R).

Parsing a file

readr uses a heuristic to figure out the type of each column: it reads the first 1000 rows and uses some (moderately conservative) heuristics to figure out the type of each column. You can emulate this process with a character vector using guess_parser(), which returns readr’s best guess, and parse_guess() which uses that guess to parse the column:

guess_parser("2010-10-01")

[1] "date"

guess_parser("15:01")

[1] "time"

guess_parser(c("TRUE", "FALSE"))

[1] "logical"

guess_parser(c("1", "5", "9"))

[1] "integer"

guess_parser(c("12,352,561"))

[1] "number"

str(parse_guess("2010-10-10"))

 Date[1:1], format: "2010-10-10"

The heuristic tries each of the following types, stopping when it finds a match:

logical: contains only “F”, “T”, “FALSE”, or “TRUE”.
integer: contains only numeric characters (and -).
double: contains only valid doubles (including numbers like 4.5e-5).
number: contains valid doubles with the grouping mark inside.
time: matches the default time_format.
date: matches the default date_format.
date-time: any ISO8601 date.

If none of these rules apply, then the column will stay as a vector of strings.

Problems

These defaults don’t always work for larger files. There are two basic problems:

The first thousand rows might be a special case, and readr guesses a type that is not sufficiently general. For example, you might have a column of doubles that only contains integers in the first 1000 rows.
The column might contain a lot of missing values. If the first 1000 rows contain only NAs, readr will guess that it’s a character vector, whereas you probably want to parse it as something more specific.

readr contains a challenging CSV that illustrates both of these problems:

head(read_csv(readr_example("challenge.csv")))

Parsed with column specification:
cols(
  x = col_integer(),
  y = col_character()
)

Warning in rbind(names(probs), probs_f): number of columns of result is not
a multiple of vector length (arg 1)

Warning: 1000 parsing failures.
row # A tibble: 5 x 5 col     row col   expected        actual      file                              expected   <int> <chr> <chr>           <chr>       <chr>                             actual 1  1001 x     no trailing ch… .238379750… '/Users/dlavrov/Library/R/3.3/li… file 2  1002 x     no trailing ch… .411679971… '/Users/dlavrov/Library/R/3.3/li… row 3  1003 x     no trailing ch… .746071676… '/Users/dlavrov/Library/R/3.3/li… col 4  1004 x     no trailing ch… .723450553… '/Users/dlavrov/Library/R/3.3/li… expected 5  1005 x     no trailing ch… .614524137… '/Users/dlavrov/Library/R/3.3/li…
... ................. ... ........................................................................... ........ ........................................................................... ...... ........................................................................... .... ........................................................................... ... ........................................................................... ... ........................................................................... ........ ...........................................................................
See problems(...) for more details.

# A tibble: 6 x 2
      x y    
  <int> <chr>
1   404 <NA> 
2  4172 <NA> 
3  3004 <NA> 
4   787 <NA> 
5    37 <NA> 
6  2332 <NA> 

challenge <- read_csv(readr_example("challenge.csv"))

Parsed with column specification:
cols(
  x = col_integer(),
  y = col_character()
)

Warning in rbind(names(probs), probs_f): number of columns of result is not a multiple of vector length (arg 1)
Warning in rbind(names(probs), probs_f): 1000 parsing failures.
row # A tibble: 5 x 5 col     row col   expected        actual      file                              expected   <int> <chr> <chr>           <chr>       <chr>                             actual 1  1001 x     no trailing ch… .238379750… '/Users/dlavrov/Library/R/3.3/li… file 2  1002 x     no trailing ch… .411679971… '/Users/dlavrov/Library/R/3.3/li… row 3  1003 x     no trailing ch… .746071676… '/Users/dlavrov/Library/R/3.3/li… col 4  1004 x     no trailing ch… .723450553… '/Users/dlavrov/Library/R/3.3/li… expected 5  1005 x     no trailing ch… .614524137… '/Users/dlavrov/Library/R/3.3/li…
... ................. ... ........................................................................... ........ ........................................................................... ...... ........................................................................... .... ........................................................................... ... ........................................................................... ... ........................................................................... ........ ...........................................................................
See problems(...) for more details.

(Note the use of readr_example() which finds the path to one of the files included with the package)

There are two printed outputs: the column specification generated by looking at the first 1000 rows, and the first five parsing failures. It’s always a good idea to explicitly pull out the problems(), so you can explore them in more depth:

problems(challenge)

# A tibble: 1,000 x 5
     row col   expected        actual      file                            
   <int> <chr> <chr>           <chr>       <chr>                           
1001 x     no trailing ch… .238379750… '/Users/dlavrov/Library/R/3.3/l…
1002 x     no trailing ch… .411679971… '/Users/dlavrov/Library/R/3.3/l…
1003 x     no trailing ch… .746071676… '/Users/dlavrov/Library/R/3.3/l…
1004 x     no trailing ch… .723450553… '/Users/dlavrov/Library/R/3.3/l…
1005 x     no trailing ch… .614524137… '/Users/dlavrov/Library/R/3.3/l…
1006 x     no trailing ch… .473980569… '/Users/dlavrov/Library/R/3.3/l…
1007 x     no trailing ch… .578461039… '/Users/dlavrov/Library/R/3.3/l…
1008 x     no trailing ch… .241593722… '/Users/dlavrov/Library/R/3.3/l…
1009 x     no trailing ch… .114378662… '/Users/dlavrov/Library/R/3.3/l…
1010 x     no trailing ch… .298344632… '/Users/dlavrov/Library/R/3.3/l…
# … with 990 more rows

A good strategy is to work column by column until there are no problems remaining. Here we can see that there are a lot of parsing problems with the x column - there are trailing characters after the integer value. That suggests we need to use a double parser instead.

To fix the call, start by copying and pasting the column specification into your original call. Then you can tweak the type of the x column:

challenge <- read_csv(
  readr_example("challenge.csv"), 
  col_types = cols(
    x = col_double(),
    y = col_character()
  )
)

That fixes the first problem, but if we look at the last few rows, you’ll see that they’re dates stored in a character vector:

tail(challenge)

# A tibble: 6 x 2
      x y         
  <dbl> <chr>     
1 0.805 2019-11-21
2 0.164 2018-03-29
3 0.472 2014-08-04
4 0.718 2015-08-16
5 0.270 2020-02-04
6 0.608 2019-01-06

You can fix that by specifying that y is a date column:

challenge <- read_csv(
  readr_example("challenge.csv"), 
  col_types = cols(
    x = col_double(),
    y = col_date()
  )
)
tail(challenge)

# A tibble: 6 x 2
      x y         
  <dbl> <date>    
1 0.805 2019-11-21
2 0.164 2018-03-29
3 0.472 2014-08-04
4 0.718 2015-08-16
5 0.270 2020-02-04
6 0.608 2019-01-06

Every parse_xyz() function has a corresponding col_xyz() function. You use parse_xyz() when the data is in a character vector in R already; you use col_xyz() when you want to tell readr how to load the data.

It’s a good idea to supply col_types from the print-out provided by readr in your read_csv call. This ensures that you have a consistent and reproducible data import script. If you rely on the default guesses and your data changes, readr will continue to read it in. If you want to be really strict, use stop_for_problems(): that will throw an error and stop your script if there are any parsing problems.

Key Points

Use read_cvs to read in CSV files

Use read_tvs to read in TSV files

Use write_csv() and write_tsv() to write such files

Supply col_types to read functions in your script to insure consistancy

Use guess_encoding() to guess encoding of strings in old docs

previous episode

R Data Skills for Bioinformatics

Data Import

next episode

Overview

Data import

Introduction

Prerequisites

Getting started

Compared to base R

Writing to a file

Other types of data

Homework

Parsing a vector (read if you run into problems or if like details)

Numbers

Strings

Parsing a file

Problems

Key Points

previous episode

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