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This lesson is in the early stages of development (Alpha version)

 Intro to R and RStudio for Genomics (../) 

(../02- (../04-
r-basics dplyr/index.html
/index.html)

R Basics continued - factors and data

frames
 Overview

TTeeaacchhiinngg:: 60 min
EExxeerrcciisseess:: 30 min
QQuueessttiioonnss
How do I get started with tabular data (e.g. spreadsheets) in R?
What are some best practices for reading data into R?
How do I save tabular data generated in R?
O
Obbjjeeccttiivveess
Explain the basic principle of tidy datasets
Be able to load a tabular dataset using base R functions
Be able to determine the structure of a data frame including its dimensions and the
datatypes of variables
Be able to subset/retrieve values from a data frame
Understand how R may coerce data into different modes
Be able to change the mode of an object
Understand that R uses factors to store and manipulate categorical data
Be able to manipulate a factor, including subsetting and reordering
Be able to apply an arithmetic function to a data frame
Be able to coerce the class of an object (including variables in a data frame)
Be able to import data from Excel
Be able to save a data frame as a delimited file

Working with spreadsheets (tabular data)

A substantial amount of the data we work with in genomics will be tabular data, this is data
arranged in rows and columns - also known as spreadsheets. We could write a whole lesson on how
to work with spreadsheets effectively (actually we did (https://datacarpentry.org/organization-
genomics/)). For our purposes, we want to remind you of a few principles before we work with our
first set of example data:

11)) K
Keeeepp rraaw
w ddaattaa sseeppaarraattee ffrroom
m aannaallyyzzeedd ddaattaa

This is principle number one because if you can’t tell which files are the original raw data, you risk
making some serious mistakes (e.g. drawing conclusion from data which have been manipulated in
some unknown way).

22)) K
Keeeepp sspprreeaaddsshheeeett ddaattaa TTiiddyy

The simplest principle of TTiiddyy ddaattaa is that we have one row in our spreadsheet for each

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observation or sample, and one column for every variable that we measure or report on. As simple
as this sounds, it’s very easily violated. Most data scientists agree that significant amounts of their
time is spent tidying data for analysis. Read more about data organization in our lesson
(https://datacarpentry.org/organization-genomics/) and in this paper (https://www.jstatsoft.org
/article/view/v059i10).

33)) TTrruusstt bbuutt vveerriiffyy

Finally, while you don’t need to be paranoid about data, you should have a plan for how you will
prepare it for analysis. TThhiiss aa ffooccuuss ooff tthhiiss lleessssoonn.. You probably already have a lot of intuition,
expectations, assumptions about your data - the range of values you expect, how many values
should have been recorded, etc. Of course, as the data get larger our human ability to keep track
will start to fail (and yes, it can fail for small data sets too). R will help you to examine your data so
that you can have greater confidence in your analysis, and its reproducibility.

 Tip: Keeping you raw data separate

When you work with data in R, you are not changing the original file you loaded that data from.
This is different than (for example) working with a spreadsheet program where changing the
value of the cell leaves you one “save”-click away from overwriting the original file. You have to
purposely use a writing function (e.g. write.csv() ) to save data loaded into R. In that case, be
sure to save the manipulated data into a new file. More on this later in the lesson.

Importing tabular data into R

There are several ways to import data into R. For our purpose here, we will focus on using the tools
every R installation comes with (so called “base” R) to import a comma-delimited file containing the
results of our variant calling workflow. We will need to load the sheet using a function called
read.csv() .

✏ Exercise: Review the arguments of the read.csv() function

BBeeffoorree uussiinngg tthhee read.csv() ffuunnccttiioonn,, uussee R

R’’ss hheellpp ffeeaattuurree ttoo aannssw
weerr tthhee ffoolllloow
wiinngg
qquueessttiioonnss.

Hint: Entering ‘?’ before the function name and then running that line will bring up the help
documentation. Also, when reading this particular help be careful to pay attention to the
‘read.csv’ expression under the ‘Usage’ heading. Other answers will be in the ‘Arguments’
heading.

A) What is the default parameter for ‘header’ in the read.csv() function?

B) What argument would you have to change to read a file that was delimited by semicolons (;)
rather than commas?

C) What argument would you have to change to read file in which numbers used commas for
decimal separation (i.e. 1,00)?

D) What argument would you have to change to read in only the first 10,000 rows of a very large
file?

 Solution 

Now, let’s read in the file combined_tidy_vcf.csv which will be located in

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/home/dcuser/.solutions/R_data/ . Call this data variants . The first argument to pass to our
read.csv() function is the file path for our data. The file path must be in quotes and now is a
good time to remember to use tab autocompletion. IIff yyoouu uussee ttaabb aauuttooccoom
mpplleettiioonn yyoouu aavvooiidd
ttyyppooss aanndd eerrrroorrss iinn fi
fillee ppaatthhss.. Use it!

R
R

## read in a CSV file and save it as 'variants'

variants <- read.csv("../r_data/combined_tidy_vcf.csv")

One of the first things you should notice is that in the Environment window, you have the
variants object, listed as 801 obs. (observations/rows) of 29 variables (columns). Double-clicking
on the name of the object will open a view of the data in a new tab.

Summarizing and determining the structure of a

data frame.
A ddaattaa ffrraam
mee iiss tthhee ssttaannddaarrdd w
waayy iinn R
R ttoo ssttoorree ttaabbuullaarr ddaattaa. A data fame could also be thought
of as a collection of vectors, all of which have the same length. Using only two functions, we can
learn a lot about out data frame including some summary statistics as well as well as the
“structure” of the data frame. Let’s examine what each of these functions can tell us:

R
R

## get summary statistics on a data frame

summary(variants)

O
Ouuttppuutt

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sample_id CHROM POS ID

Length:801 Length:801 Min. : 1521 Mode:logical
Class :character Class :character 1st Qu.:1115970 NA's:801
Mode :character Mode :character Median :2290361
Mean :2243682
3rd Qu.:3317082
Max. :4629225

REF ALT QUAL FILTER

Length:801 Length:801 Min. : 4.385 Mode:logical
Class :character Class :character 1st Qu.:139.000 NA's:801
Mode :character Mode :character Median :195.000
Mean :172.276
3rd Qu.:225.000
Max. :228.000

INDEL IDV IMF DP

Mode :logical Min. : 2.000 Min. :0.5714 Min. : 2.00
FALSE:700 1st Qu.: 7.000 1st Qu.:0.8824 1st Qu.: 7.00
TRUE :101 Median : 9.000 Median :1.0000 Median :10.00
Mean : 9.396 Mean :0.9219 Mean :10.57
3rd Qu.:11.000 3rd Qu.:1.0000 3rd Qu.:13.00
Max. :20.000 Max. :1.0000 Max. :79.00
NA's :700 NA's :700
VDB RPB MQB BQB
Min. :0.0005387 Min. :0.0000 Min. :0.0000 Min. :0.1153
1st Qu.:0.2180410 1st Qu.:0.3776 1st Qu.:0.1070 1st Qu.:0.6963
Median :0.4827410 Median :0.8663 Median :0.2872 Median :0.8615
Mean :0.4926291 Mean :0.6970 Mean :0.5330 Mean :0.7784
3rd Qu.:0.7598940 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:1.0000
Max. :0.9997130 Max. :1.0000 Max. :1.0000 Max. :1.0000
NA's :773 NA's :773 NA's :773
MQSB SGB MQ0F ICB
Min. :0.01348 Min. :-0.6931 Min. :0.00000 Mode:logical
1st Qu.:0.95494 1st Qu.:-0.6762 1st Qu.:0.00000 NA's:801
Median :1.00000 Median :-0.6620 Median :0.00000
Mean :0.96428 Mean :-0.6444 Mean :0.01127
3rd Qu.:1.00000 3rd Qu.:-0.6364 3rd Qu.:0.00000
Max. :1.01283 Max. :-0.4536 Max. :0.66667
NA's :48
HOB AC AN DP4 MQ
Mode:logical Min. :1 Min. :1 Length:801 Min. :10.00
NA's:801 1st Qu.:1 1st Qu.:1 Class :character 1st Qu.:60.00
Median :1 Median :1 Mode :character Median :60.00
Mean :1 Mean :1 Mean :58.19
3rd Qu.:1 3rd Qu.:1 3rd Qu.:60.00
Max. :1 Max. :1 Max. :60.00

Indiv gt_PL gt_GT gt_GT_alleles

Length:801 Length:801 Min. :1 Length:801
Class :character Class :character 1st Qu.:1 Class :character
Mode :character Mode :character Median :1 Mode :character
Mean :1
3rd Qu.:1
Max. :1

Our data frame had 29 variables, so we get 29 fields that summarize the data. The QUAL , IMF , and
VDB variables (and several others) are numerical data and so you get summary statistics on the
min and max values for these columns, as well as mean, median, and interquartile ranges. Many of
the other variables (e.g. sample_id ) are treated as categorical data (which have special treatment
in R - more on this in a bit). The most frequent 6 different categories and the number of times they
appear (e.g. the sample_id called ‘SRR2584863’ appeared 25 times) are displayed. There was only
one value for CHROM , “CP000819.1” which appeared in all 801 observations.

Before we operate on the data, we also need to know a little more about the data frame structure
to do that we use the str() function:

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R
R

## get the structure of a data frame

str(variants)

O
Ouuttppuutt

'data.frame': 801 obs. of 29 variables:

$ sample_id : chr "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863" ...
$ CHROM : chr "CP000819.1" "CP000819.1" "CP000819.1" "CP000819.1" ...
$ POS : int 9972 263235 281923 433359 473901 648692 1331794 1733343 2103887 2
333538 ...
$ ID : logi NA NA NA NA NA NA ...
$ REF : chr "T" "G" "G" "CTTTTTTT" ...
$ ALT : chr "G" "T" "T" "CTTTTTTTT" ...
$ QUAL : num 91 85 217 64 228 210 178 225 56 167 ...
$ FILTER : logi NA NA NA NA NA NA ...
$ INDEL : logi FALSE FALSE FALSE TRUE TRUE FALSE ...
$ IDV : int NA NA NA 12 9 NA NA NA 2 7 ...
$ IMF : num NA NA NA 1 0.9 ...
$ DP : int 4 6 10 12 10 10 8 11 3 7 ...
$ VDB : num 0.0257 0.0961 0.7741 0.4777 0.6595 ...
$ RPB : num NA 1 NA NA NA NA NA NA NA NA ...
$ MQB : num NA 1 NA NA NA NA NA NA NA NA ...
$ BQB : num NA 1 NA NA NA NA NA NA NA NA ...
$ MQSB : num NA NA 0.975 1 0.916 ...
$ SGB : num -0.556 -0.591 -0.662 -0.676 -0.662 ...
$ MQ0F : num 0 0.167 0 0 0 ...
$ ICB : logi NA NA NA NA NA NA ...
$ HOB : logi NA NA NA NA NA NA ...
$ AC : int 1 1 1 1 1 1 1 1 1 1 ...
$ AN : int 1 1 1 1 1 1 1 1 1 1 ...
$ DP4 : chr "0,0,0,4" "0,1,0,5" "0,0,4,5" "0,1,3,8" ...
$ MQ : int 60 33 60 60 60 60 60 60 60 60 ...
$ Indiv : chr "/home/dcuser/dc_workshop/results/bam/SRR2584863.aligned.sorted.b
am" "/home/dcuser/dc_workshop/results/bam/SRR2584863.aligned.sorted.bam" "/home/dcuser/d
c_workshop/results/bam/SRR2584863.aligned.sorted.bam" "/home/dcuser/dc_workshop/results/
bam/SRR2584863.aligned.sorted.bam" ...
$ gt_PL : chr "121,0" "112,0" "247,0" "91,0" ...
$ gt_GT : int 1 1 1 1 1 1 1 1 1 1 ...
$ gt_GT_alleles: chr "G" "T" "T" "CTTTTTTTT" ...

Ok, thats a lot up unpack! Some things to notice.

the object type data.frame is displayed in the first row along with its dimensions, in this case
801 observations (rows) and 29 variables (columns)
Each variable (column) has a name (e.g. sample_id ). This is followed by the object mode (e.g.
factor, int, num, etc.). Notice that before each variable name there is a $ - this will be
important later.

Introducing Factors
Factors are the final major data structure we will introduce in our R genomics lessons. Factors can
be thought of as vectors which are specialized for categorical data. Given R’s specialization for
statistics, this make sense since categorial and continuous variables usually have different
treatments. Sometimes you may want to have data treated as a factor, but in other cases, this may
be undesirable.

Since some of the data in our data frame are factors, lets see how factors work. First, we’ll extract
one of the columns of our data frame to a new object, so that we don’t end up modifying the
variants object by mistake.

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R
R

## extract the "REF" column to a new object

REF <- variants$REF

Let’s look at the first few items in our factor using head() :

R
R

head(REF)

O
Ouuttppuutt

[1] "T" "G" "G" "CTTTTTTT" "CCGC" "C"

What we get back are the items in our factor, and also something called “Levels”. LLeevveellss aarree tthhee
ddiiff
ffeerreenntt ccaatteeggoorriieess ccoonnttaaiinneedd iinn aa ffaaccttoorr. By default, R will organize the levels in a factor in
alphabetical order. So the first level in this factor is “A”.

Lets look at the contents of a factor in a slightly different way using str() :

R
R

str(REF)

O
Ouuttppuutt

chr [1:801] "T" "G" "G" "CTTTTTTT" "CCGC" "C" "C" "G" ...

For the sake of efficiency, R stores the content of a factor as a vector of integers, which an integer
is assigned to each of the possible levels. Recall levels are assigned in alphabetical order. In this
case, the first item in our “REF” object is “T”, which happens to be the 49th level of our factor,
ordered alphabeticaly. The next two items are both “G”s, which is the 33rd level of our factor.

Plotting and ordering factors

One of the most common uses for factors will be when you plot categorical values. For example,
suppose we want to know how many of our variants had each possible nucleotide (or nucleotide
combination) in the reference genome? We could generate a plot:

R
R

plot(REF)

W
Waarrnniinngg

Warning in xy.coords(x, y, xlabel, ylabel, log): NAs introduced by coercion

W
Waarrnniinngg

Warning in min(x): no non-missing arguments to min; returning Inf

W
Waarrnniinngg

Warning in max(x): no non-missing arguments to max; returning -Inf

EErrrroorr

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Error in plot.window(...): need finite 'ylim' values

This isn’t a particularly pretty example of a plot. We’ll be learning much more about creating nice,
publication-quality graphics later in this lesson.

Subsetting data frames

Next, we are going to talk about how you can get specific values from data frames, and where
necessary, change the mode of a column of values.

The first thing to remember is that a data frame is two-dimensional (rows and columns). Therefore,
to select a specific value we will will once again use [] (bracket) notation, but we will specify more
than one value (except in some cases where we are taking a range).

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✏ Exercise: Subsetting a data frame

TTrryy tthhee ffoolllloow

wiinngg iinnddiicceess aanndd ffuunnccttiioonnss aanndd ttrryy ttoo fi
figguurree oouutt w
whhaatt tthheeyy rreettuurrnn

a. variants[1,1]

b. variants[2,4]

c. variants[801,29]

d. variants[2, ]

e. variants[-1, ]

f. variants[1:4,1]

g. variants[1:10,c("REF","ALT")]

h. variants[,c("sample_id")]

i. head(variants)

j. tail(variants)

k. variants$sample_id

l. variants[variants$REF == "A",]

 Solution 

The subsetting notation is very similar to what we learned for vectors. The key differences include:

Typically provide two values separated by commas: data.frame[row, column]

In cases where you are taking a continuous range of numbers use a colon between the
numbers (start:stop, inclusive)
For a non continuous set of numbers, pass a vector using c()
Index using the name of a column(s) by passing them as vectors using c()

Finally, in all of the subsetting exercises above, we printed values to the screen. You can create a
new data frame object by assigning them to a new object name:

R
R

# create a new data frame containing only observations from SRR2584863

SRR2584863_variants <- variants[variants$sample_id == "SRR2584863",]

# check the dimension of the data frame

dim(SRR2584863_variants)

O
Ouuttppuutt

[1] 25 29

R
R

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# get a summary of the data frame

summary(SRR2584863_variants)

O
Ouuttppuutt

sample_id CHROM POS ID

Length:25 Length:25 Min. : 9972 Mode:logical
Class :character Class :character 1st Qu.:1331794 NA's:25
Mode :character Mode :character Median :2618472
Mean :2464989
3rd Qu.:3488669
Max. :4616538

REF ALT QUAL FILTER

Length:25 Length:25 Min. : 31.89 Mode:logical
Class :character Class :character 1st Qu.:104.00 NA's:25
Mode :character Mode :character Median :211.00
Mean :172.97
3rd Qu.:225.00
Max. :228.00

INDEL IDV IMF DP

Mode :logical Min. : 2.00 Min. :0.6667 Min. : 2.0
FALSE:19 1st Qu.: 3.25 1st Qu.:0.9250 1st Qu.: 9.0
TRUE :6 Median : 8.00 Median :1.0000 Median :10.0
Mean : 7.00 Mean :0.9278 Mean :10.4
3rd Qu.: 9.75 3rd Qu.:1.0000 3rd Qu.:12.0
Max. :12.00 Max. :1.0000 Max. :20.0
NA's :19 NA's :19
VDB RPB MQB BQB
Min. :0.01627 Min. :0.9008 Min. :0.04979 Min. :0.7507
1st Qu.:0.07140 1st Qu.:0.9275 1st Qu.:0.09996 1st Qu.:0.7627
Median :0.37674 Median :0.9542 Median :0.15013 Median :0.7748
Mean :0.40429 Mean :0.9517 Mean :0.39997 Mean :0.8418
3rd Qu.:0.65951 3rd Qu.:0.9771 3rd Qu.:0.57507 3rd Qu.:0.8874
Max. :0.99604 Max. :1.0000 Max. :1.00000 Max. :1.0000
NA's :22 NA's :22 NA's :22
MQSB SGB MQ0F ICB
Min. :0.5000 Min. :-0.6904 Min. :0.00000 Mode:logical
1st Qu.:0.9599 1st Qu.:-0.6762 1st Qu.:0.00000 NA's:25
Median :0.9962 Median :-0.6620 Median :0.00000
Mean :0.9442 Mean :-0.6341 Mean :0.04667
3rd Qu.:1.0000 3rd Qu.:-0.6168 3rd Qu.:0.00000
Max. :1.0128 Max. :-0.4536 Max. :0.66667
NA's :3
HOB AC AN DP4 MQ
Mode:logical Min. :1 Min. :1 Length:25 Min. :10.00
NA's:25 1st Qu.:1 1st Qu.:1 Class :character 1st Qu.:60.00
Median :1 Median :1 Mode :character Median :60.00
Mean :1 Mean :1 Mean :55.52
3rd Qu.:1 3rd Qu.:1 3rd Qu.:60.00
Max. :1 Max. :1 Max. :60.00

Indiv gt_PL gt_GT gt_GT_alleles

Length:25 Length:25 Min. :1 Length:25
Class :character Class :character 1st Qu.:1 Class :character
Mode :character Mode :character Median :1 Mode :character
Mean :1
3rd Qu.:1
Max. :1

Coercing values in data frames

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 Tip: coercion isn’t limited to data frames

While we are going to address coercion in the context of data frames most of these methods
apply to other data structures, such as vectors

Sometimes, it is possible that R will misinterpret the type of data represented in a data frame, or
store that data in a mode which prevents you from operating on the data the way you wish. For
example, a long list of gene names isn’t usually thought of as a categorical variable, the way that
your experimental condition (e.g. control, treatment) might be. More importantly, some R packages
you use to analyze your data may expect characters as input, not factors. At other times (such as
plotting or some statistical analyses) a factor may be more appropriate. Ultimately, you should
know how to change the mode of an object.

First, its very important to recognize that coercion happens in R all the time. This can be a good
thing when R gets it right, or a bad thing when the result is not what you expect. Consider:

R
R

snp_chromosomes <- c('3', '11', 'X', '6')

typeof(snp_chromosomes)

O
Ouuttppuutt

[1] "character"

Although there are several numbers in our vector, they are all in quotes, so we have explicitly told R
to consider them as characters. However, even if we removed the quotes from the numbers, R
would coerce everything into a character:

R
R

snp_chromosomes_2 <- c(3, 11, 'X', 6)

typeof(snp_chromosomes_2)

O
Ouuttppuutt

[1] "character"

R
R

snp_chromosomes_2[1]

O
Ouuttppuutt

[1] "3"

We can use the as. functions to explicitly coerce values from one form into another. Consider the
following vector of characters, which all happen to be valid numbers:

R
R

snp_positions_2 <- c("8762685", "66560624", "67545785", "154039662")

typeof(snp_positions_2)

O
Ouuttppuutt

[1] "character"

R
R

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snp_positions_2[1]

O
Ouuttppuutt

[1] "8762685"

Now we can coerce snp_positions_2 into a numeric type using as.numeric() :

R
R

snp_positions_2 <- as.numeric(snp_positions_2)

typeof(snp_positions_2)

O
Ouuttppuutt

[1] "double"

R
R

snp_positions_2[1]

O
Ouuttppuutt

[1] 8762685

Sometimes coercion is straight forward, but what would happen if we tried using as.numeric()
on snp_chromosomes_2

R
R

snp_chromosomes_2 <- as.numeric(snp_chromosomes_2)

W
Waarrnniinngg

Warning: NAs introduced by coercion

If we check, we will see that an NA value (R’s default value for missing data) has been introduced.

R
R

snp_chromosomes_2

O
Ouuttppuutt

[1] 3 11 NA 6

Trouble can really start when we try to coerce a factor. For example, when we try to coerce the
sample_id column in our data frame into a numeric mode look at the result:

R
R

as.numeric(variants$sample_id)

W
Waarrnniinngg

Warning: NAs introduced by coercion

O
Ouuttppuutt

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[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[101] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[126] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[151] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[176] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[201] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[226] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[251] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[276] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[301] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[326] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[351] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[376] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[401] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[426] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[451] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[476] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[501] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[526] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[551] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[576] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[601] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[626] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[651] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[676] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[701] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[726] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[751] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[776] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[801] NA

Strangely, it works! Almost. Instead of giving an error message, R returns numeric values, which in
this case are the integers assigned to the levels in this factor. This kind of behavior can lead to hard-
to-find bugs, for example when we do have numbers in a factor, and we get numbers from a
coercion. If we don’t look carefully, we may not notice a problem.

If you need to coerce an entire column you can overwrite it using an expression like this one:

R
R

# make the 'REF' column a character type column

variants$REF <- as.character(variants$REF)

# check the type of the column

typeof(variants$REF)

O
Ouuttppuutt

[1] "character"

StringsAsFactors = FALSE
Lets summarize this section on coercion with a few take home messages.

When you explicitly coerce one data type into another (this is known as eexxpplliicciitt ccooeerrcciioonn), be
careful to check the result. Ideally, you should try to see if its possible to avoid steps in your
analysis that force you to coerce.
R will sometimes coerce without you asking for it. This is called (appropriately) iim mpplliicciitt
ccooeerrcciioonn. For example when we tried to create a vector with multiple data types, R chose one

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type through implicit coercion.

Check the structure ( str() ) of your data frames before working with them!

Regarding the first bullet point, one way to avoid needless coercion when importing a data frame
using any one of the read.table() functions such as read.csv() is to set the argument
StringsAsFactors to FALSE. By default, this argument is TRUE. Setting it to FALSE will treat any
non-numeric column to a character type. read.csv() documentation, you will also see you can
explicitly type your columns using the colClasses argument. Other R packages (such as the
Tidyverse “readr”) don’t have this particular conversion issue, but many packages will still try to
guess a data type.

Data frame bonus material: math, sorting, renaming

Here are a few operations that don’t need much explanation, but which are good to know.

There are lots of arithmetic functions you may want to apply to your data frame, covering those
would be a course in itself (there is some starting material here (https://swcarpentry.github.io/r-
novice-inflammation/15-supp-loops-in-depth/)). Our lessons will cover some additional summary
statistical functions in a subsequent lesson, but overall we will focus on data cleaning and
visualization.

You can use functions like mean() , min() , max() on an individual column. Let’s look at the “DP”
or filtered depth. This value shows the number of filtered reads that support each of the reported
variants.

R
R

max(variants$DP)

O
Ouuttppuutt

[1] 79

You can sort a data frame using the order() function:

R
R

sorted_by_DP <- variants[order(variants$DP), ]

head(sorted_by_DP$DP)

O
Ouuttppuutt

[1] 2 2 2 2 2 2

✏ Exercise

The order() function lists values in increasing order by default. Look at the documentation for
this function and change sorted_by_DP to start with variants with the greatest filtered depth
(“DP”).

 Solution 

You can rename columns:

R
R

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colnames(variants)[colnames(variants) == "sample_id"] <- "strain"

# check the column name (hint names are returned as a vector)

colnames(variants)

O
Ouuttppuutt

[1] "strain" "CHROM" "POS" "ID"

[5] "REF" "ALT" "QUAL" "FILTER"
[9] "INDEL" "IDV" "IMF" "DP"
[13] "VDB" "RPB" "MQB" "BQB"
[17] "MQSB" "SGB" "MQ0F" "ICB"
[21] "HOB" "AC" "AN" "DP4"
[25] "MQ" "Indiv" "gt_PL" "gt_GT"
[29] "gt_GT_alleles"

Saving your data frame to a file

We can save data to a file. We will save our SRR2584863_variants object to a .csv file using the
write.csv() function:

R
R

write.csv(SRR2584863_variants, file = "../data/SRR2584863_variants.csv")

The write.csv() function has some additional arguments listed in the help, but at a minimum
you need to tell it what data frame to write to file, and give a path to a file name in quotes (if you
only provide a file name, the file will be written in the current working directory).

Importing data from Excel

Excel is one of the most common formats, so we need to discuss how to make these files play nicely
with R. The simplest way to import data from Excel is to ssaavvee yyoouurr EExxcceell fi
fillee iinn ..ccssvv ffoorrm
maatt*. You
can then import into R right away. Sometimes you may not be able to do this (imagine you have
data in 300 Excel files, are you going to open and export all of them?).

One common R package (a set of code with features you can download and add to your R
installation) is the readxl package (https://CRAN.R-project.org/package=readxl) which can open and
import Excel files. Rather than addressing package installation this second (we’ll discuss this soon!),
we can take advantage of RStudio’s import feature which integrates this package. (Note: this
feature is available only in the latest versions of RStudio such as is installed on our cloud instance).

First, in the RStudio menu go to FFiillee, select IIm

mppoorrtt D
Daattaasseett, and choose FFrroom
m EExxcceell…
… (notice
there are several other options you can explore).

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Next, under FFiillee//U

Urrll:: click the Browse button and navigate to the EEccoollii__m
meettaaddaattaa..xxllssxx file located
at /home/dcuser/dc_sample_data/R . You should now see a preview of the data to be imported:

Notice that you have the option to change the data type of each variable by clicking arrow (drop-
down menu) next to each column title. Under IIm mppoorrtt O
Oppttiioonnss you may also rename the data,
choose a different sheet to import, and choose how you will handle headers and skipped rows.
Under CCooddee PPrreevviieew
w you can see the code that will be used to import this file. We could have
written this code and imported the Excel file without the RStudio import function, but now you can
choose your preference.

In this exercise, we will leave the title of the data frame as EEccoollii__m
meettaaddaattaa, and there are no other
options we need to adjust. Click the Import button to import the data.

Finally, let’s check the first few lines of the Ecoli_metadata data frame:

EErrrroorr

Error: `path` does not exist: '../data/Ecoli_metadata.xlsx'

R
R

head(Ecoli_metadata)

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EErrrroorr

Error in head(Ecoli_metadata): object 'Ecoli_metadata' not found

The type of this object is ‘tibble’, a type of data frame we will talk more about in the ‘dplyr’ section.
If you needed a true R data frame you could coerce with as.data.frame() .

✏ Exercise: Putting it all together - data frames

U
Ussiinngg tthhee Ecoli_metadata ddaattaa ffrraam
mee ccrreeaatteedd aabboovvee,, aannssw
weerr tthhee ffoolllloow
wiinngg qquueessttiioonnss

A) What are the dimensions (# rows, # columns) of the data frame?

B) What are categories are there in the cit column? hint: treat column as factor

C) How many of each of the cit categories are there?

D) What is the genome size for the 7th observation in this data set?

E) What is the median value of the variable genome_size

F) Rename the column sample to sample_id

G) Create a new column (name genome_size_bp) and set it equal to the genome_size multiplied
by 1,000,000

H) Save the edited Ecoli_metadata data frame as “exercise_solution.csv” in your current working
directory.

 Solution 

 Key Points

It is easy to import data into R from tabular formats including Excel. However, you still need
to check that R has imported and interpreted your data correctly
There are best practices for organizing your data (keeping it tidy) and R is great for this
Base R has many useful functions for manipulating your data, but all of R’s capabilities are
greatly enhanced by software packages developed by the community

 
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