Chapter 6 Joining tables

Learning Objectives:

  • Understand the need and concept of table joins

  • Understand the different types of joins

  • Understand the importance of keys in joins and the implications of using non-unique keys

In many real life situations, data are spread across multiple tables. Usually this occurs because different types of information about a subject, e.g. a patient, are collected from different sources.

It may be desirable for some analyses to combine data from two or more tables into a single data frame based on a column that would be common to all the tables, for example, an attribute that uniquely identifies the subjects.

The dplyr package provides a set of join functions for combining two data frames based on matches within specified columns.

For further reading, please refer to the chapter about table joins in Grolemund and Wickham (2017Grolemund, Garrett, and Hadley Wickham. 2017. R for Data Science. O’Reilly Media. https://r4ds.had.co.nz/.).

The Data Transformation Cheat Sheet also provides a short overview on table joins.

6.1 Combining tables

We are going to illustrate join using a common example from the bioinformatics world, where annotations about genes are scattered in different tables that have one or more shared columns.

The data we are going to use are available in the following package.

# install.packages(c("BiocManager", "remotes"))
# BiocManager::install("UCLouvain-CBIO/rWSBIM1207")
library("rWSBIM1207")
## 
## This is 'rWSBIM1207' version 0.1.19
data(jdf)

The data is composed of several tables.

The first table, jdf1, contains protein UniProt8 UniProt is the protein information database. Its mission is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. unique accession number (uniprot variable), the most likely sub-cellular localisation of these respective proteins (organelle variable) as well as the proteins identifier (entry).

jdf1
## # A tibble: 25 × 3
##    uniprot  organelle                             entry      
##    <chr>    <chr>                                 <chr>      
##  1 P26039   Actin cytoskeleton                    TLN1_MOUSE 
##  2 Q99PL5   Endoplasmic reticulum/Golgi apparatus RRBP1_MOUSE
##  3 Q6PB66   Mitochondrion                         LPPRC_MOUSE
##  4 P11276   Extracellular matrix                  FINC_MOUSE 
##  5 Q6PR54   Nucleus - Chromatin                   RIF1_MOUSE 
##  6 Q05793   Extracellular matrix                  PGBM_MOUSE 
##  7 P19096   Cytosol                               FAS_MOUSE  
##  8 Q9JKF1   Plasma membrane                       IQGA1_MOUSE
##  9 Q9QZQ1-2 Plasma membrane                       AFAD_MOUSE 
## 10 Q6NS46   Nucleus - Non-chromatin               RRP5_MOUSE 
## # ℹ 15 more rows

The second table, jdf2, contains the name of the gene that codes for the protein (gene_name variable), a description of the gene (description variable), the uniprot accession number (this is the common variable that can be used to join tables) and the species the protein information comes from (organism variable).

jdf2
## # A tibble: 25 × 4
##    gene_name description                                      uniprot organism
##    <chr>     <chr>                                            <chr>   <chr>   
##  1 Iqgap1    Ras GTPase-activating-like protein IQGAP1        Q9JKF1  Mmus    
##  2 Hspa5     78 kDa glucose-regulated protein                 P20029  Mmus    
##  3 Pdcd11    Protein RRP5 homolog                             Q6NS46  Mmus    
##  4 Tfrc      Transferrin receptor protein 1                   Q62351  Mmus    
##  5 Hspd1     60 kDa heat shock protein, mitochondrial         P63038  Mmus    
##  6 Tln1      Talin-1                                          P26039  Mmus    
##  7 Smc1a     Structural maintenance of chromosomes protein 1A Q9CU62  Mmus    
##  8 Lamc1     Laminin subunit gamma-1                          P02468  Mmus    
##  9 Hsp90b1   Endoplasmin                                      P08113  Mmus    
## 10 Mia3      Melanoma inhibitory activity protein 3           Q8BI84  Mmus    
## # ℹ 15 more rows

We now want to join these two tables into a single one containing all variables.

We are going to use the full_join function of dplyr to do so,

Th function will automatically find the common variable (in this case uniprot) to match observations from the first and second table.

library("dplyr")
full_join(jdf1, jdf2)
## Joining with `by = join_by(uniprot)`
## # A tibble: 25 × 6
##    uniprot  organelle                       entry gene_name description organism
##    <chr>    <chr>                           <chr> <chr>     <chr>       <chr>   
##  1 P26039   Actin cytoskeleton              TLN1… Tln1      Talin-1     Mmus    
##  2 Q99PL5   Endoplasmic reticulum/Golgi ap… RRBP… Rrbp1     Ribosome-b… Mmus    
##  3 Q6PB66   Mitochondrion                   LPPR… Lrpprc    Leucine-ri… Mmus    
##  4 P11276   Extracellular matrix            FINC… Fn1       Fibronectin Mmus    
##  5 Q6PR54   Nucleus - Chromatin             RIF1… Rif1      Telomere-a… Mmus    
##  6 Q05793   Extracellular matrix            PGBM… Hspg2     Basement m… Mmus    
##  7 P19096   Cytosol                         FAS_… Fasn      Fatty acid… Mmus    
##  8 Q9JKF1   Plasma membrane                 IQGA… Iqgap1    Ras GTPase… Mmus    
##  9 Q9QZQ1-2 Plasma membrane                 AFAD… Mllt4     Isoform 1 … Mmus    
## 10 Q6NS46   Nucleus - Non-chromatin         RRP5… Pdcd11    Protein RR… Mmus    
## # ℹ 15 more rows

In these examples, each observation of the jdf1 and jdf2 tables are uniquely identified by their UniProt accession number. Such variables are called keys. Keys are used to match observations across different tables.

Now let’s look at a third table, jdf3. It also contains the column uniProt, but it is written diffently!

jdf3
## # A tibble: 25 × 4
##    gene_name description                                      UniProt organism
##    <chr>     <chr>                                            <chr>   <chr>   
##  1 Iqgap1    Ras GTPase-activating-like protein IQGAP1        Q9JKF1  Mmus    
##  2 Hspa5     78 kDa glucose-regulated protein                 P20029  Mmus    
##  3 Pdcd11    Protein RRP5 homolog                             Q6NS46  Mmus    
##  4 Tfrc      Transferrin receptor protein 1                   Q62351  Mmus    
##  5 Hspd1     60 kDa heat shock protein, mitochondrial         P63038  Mmus    
##  6 Tln1      Talin-1                                          P26039  Mmus    
##  7 Smc1a     Structural maintenance of chromosomes protein 1A Q9CU62  Mmus    
##  8 Lamc1     Laminin subunit gamma-1                          P02468  Mmus    
##  9 Hsp90b1   Endoplasmin                                      P08113  Mmus    
## 10 Mia3      Melanoma inhibitory activity protein 3           Q8BI84  Mmus    
## # ℹ 15 more rows

In case none of the variable names match, we can set manually the variables to use for the matching. These variables can be set using the by argument, as shown below with the jdf1 (as above) and jdf3 tables, where the UniProt accession number is encoded using a different capitalisation.

names(jdf3)
## [1] "gene_name"   "description" "UniProt"     "organism"
full_join(jdf1, jdf3, by = c("uniprot" = "UniProt"))
## # A tibble: 25 × 6
##    uniprot  organelle                       entry gene_name description organism
##    <chr>    <chr>                           <chr> <chr>     <chr>       <chr>   
##  1 P26039   Actin cytoskeleton              TLN1… Tln1      Talin-1     Mmus    
##  2 Q99PL5   Endoplasmic reticulum/Golgi ap… RRBP… Rrbp1     Ribosome-b… Mmus    
##  3 Q6PB66   Mitochondrion                   LPPR… Lrpprc    Leucine-ri… Mmus    
##  4 P11276   Extracellular matrix            FINC… Fn1       Fibronectin Mmus    
##  5 Q6PR54   Nucleus - Chromatin             RIF1… Rif1      Telomere-a… Mmus    
##  6 Q05793   Extracellular matrix            PGBM… Hspg2     Basement m… Mmus    
##  7 P19096   Cytosol                         FAS_… Fasn      Fatty acid… Mmus    
##  8 Q9JKF1   Plasma membrane                 IQGA… Iqgap1    Ras GTPase… Mmus    
##  9 Q9QZQ1-2 Plasma membrane                 AFAD… Mllt4     Isoform 1 … Mmus    
## 10 Q6NS46   Nucleus - Non-chromatin         RRP5… Pdcd11    Protein RR… Mmus    
## # ℹ 15 more rows

As can be seen above, the variable name of the first table is retained in the joined one.

► Question

Using the full_join function, join tables jdf4 and jdf5. What has happened for observations P26039 and P02468?

► Solution

6.2 Different types of joins

Above, we have used the full_join function, that fully joins two tables and keeps all observations, adding missing values if necessary. Sometimes, we want to be selective, and keep observations that are present in only one or both tables.

  • An inner join keeps observations that are present in both tables.

Figure 6.1: An inner join matches pairs of observation matching in both tables, this dropping those that are unique to one table. Figure taken from R for Data Science.

An inner join matches pairs of observation matching in both tables, this dropping those that are unique to one table. Figure taken from *R for Data Science*.
  • A left join keeps observations that are present in the left (first) table, dropping those that are only present in the other.
  • A right join keeps observations that are present in the right (second) table, dropping those that are only present in the other.
  • A full join keeps all observations.

Figure 6.2: Outer joins match observations that appear in at least on table, filling up missing values with NA values. Figure taken from R for Data Science.

Outer joins match observations that appear in at least on table, filling up missing values with `NA` values. Figure taken from *R for Data Science*.

► Question

Join tables jdf4 and jdf5, keeping only observations in jdf4.

► Solution

► Question

Join tables jdf4 and jdf5, keeping only observations in jdf5.

► Solution

► Question

Join tables jdf4 and jdf5, keeping observations observed in both tables.

► Solution

6.3 Multiple matches

Sometimes, keys aren’t unique.

In the jdf6 table below, we see that the accession number Q99PL5 is repeated twice. According to this table, the ribosomial protein binding protein 1 localises in the endoplasmic reticulum and in the Golgi apparatus.

jdf6
## # A tibble: 5 × 4
##   uniprot organelle             entry       isoform
##   <chr>   <chr>                 <chr>         <dbl>
## 1 P26039  Actin cytoskeleton    TLN1_MOUSE        1
## 2 Q99PL5  Endoplasmic reticulum RRBP1_MOUSE       1
## 3 Q99PL5  Golgi apparatus       RRBP1_MOUSE       2
## 4 Q6PB66  Mitochondrion         LPPRC_MOUSE       1
## 5 P11276  Extracellular matrix  FINC_MOUSE        1

If we now want to join jdf6 and jdf2, the variables of the latter will be duplicated.

inner_join(jdf6, jdf2)
## Joining with `by = join_by(uniprot)`
## # A tibble: 5 × 7
##   uniprot organelle             entry     isoform gene_name description organism
##   <chr>   <chr>                 <chr>       <dbl> <chr>     <chr>       <chr>   
## 1 P26039  Actin cytoskeleton    TLN1_MOU…       1 Tln1      Talin-1     Mmus    
## 2 Q99PL5  Endoplasmic reticulum RRBP1_MO…       1 Rrbp1     Ribosome-b… Mmus    
## 3 Q99PL5  Golgi apparatus       RRBP1_MO…       2 Rrbp1     Ribosome-b… Mmus    
## 4 Q6PB66  Mitochondrion         LPPRC_MO…       1 Lrpprc    Leucine-ri… Mmus    
## 5 P11276  Extracellular matrix  FINC_MOU…       1 Fn1       Fibronectin Mmus

In the case above, repeating is useful, as it completes jdf6 with correct information from jdf2.

But one needs however to be careful when duplicated keys exist in both tables.

Let’s now use jdf7 for the join. It also has 2 entries for the uniprot Q99PL5

jdf7
## # A tibble: 5 × 6
##   gene_name description                     uniprot organism isoform_num measure
##   <chr>     <chr>                           <chr>   <chr>          <dbl>   <dbl>
## 1 Rrbp1     Ribosome-binding protein 1      Q99PL5  Mmus               1     102
## 2 Rrbp1     Ribosome-binding protein 1      Q99PL5  Mmus               2       3
## 3 Iqgap1    Ras GTPase-activating-like pro… Q9JKF1  Mmus               1      13
## 4 Hspa5     78 kDa glucose-regulated prote… P20029  Mmus               1      54
## 5 Pdcd11    Protein RRP5 homolog            Q6NS46  Mmus               1      28

Let’s we create an inner join between jdf6 and jdf7 (both having duplicated Q99PL5 entries)

inner_join(jdf6, jdf7)
## Joining with `by = join_by(uniprot)`
## Warning in inner_join(jdf6, jdf7): Detected an unexpected many-to-many relationship between `x` and `y`.
## ℹ Row 2 of `x` matches multiple rows in `y`.
## ℹ Row 1 of `y` matches multiple rows in `x`.
## ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence this warning.
## # A tibble: 4 × 9
##   uniprot organelle     entry isoform gene_name description organism isoform_num
##   <chr>   <chr>         <chr>   <dbl> <chr>     <chr>       <chr>          <dbl>
## 1 Q99PL5  Endoplasmic … RRBP…       1 Rrbp1     Ribosome-b… Mmus               1
## 2 Q99PL5  Endoplasmic … RRBP…       1 Rrbp1     Ribosome-b… Mmus               2
## 3 Q99PL5  Golgi appara… RRBP…       2 Rrbp1     Ribosome-b… Mmus               1
## 4 Q99PL5  Golgi appara… RRBP…       2 Rrbp1     Ribosome-b… Mmus               2
## # ℹ 1 more variable: measure <dbl>

► Question

Interpret the result of the inner join above, where both tables have duplicated keys.

► Solution

6.4 Matching across multiple keys

So far, we have matched tables using a single key (possibly with different names in the two tables). Sometimes, it is necessary to match tables using multiple keys. A typical example is when multiple variables are needed to discriminate different rows in a tables.

Following up from the last example, we see that the duplicated UniProt accession numbers in the jdf6 and jdf7 tables refer to different isoforms of the same RRBP1 gene.

jdf6
## # A tibble: 5 × 4
##   uniprot organelle             entry       isoform
##   <chr>   <chr>                 <chr>         <dbl>
## 1 P26039  Actin cytoskeleton    TLN1_MOUSE        1
## 2 Q99PL5  Endoplasmic reticulum RRBP1_MOUSE       1
## 3 Q99PL5  Golgi apparatus       RRBP1_MOUSE       2
## 4 Q6PB66  Mitochondrion         LPPRC_MOUSE       1
## 5 P11276  Extracellular matrix  FINC_MOUSE        1
jdf7
## # A tibble: 5 × 6
##   gene_name description                     uniprot organism isoform_num measure
##   <chr>     <chr>                           <chr>   <chr>          <dbl>   <dbl>
## 1 Rrbp1     Ribosome-binding protein 1      Q99PL5  Mmus               1     102
## 2 Rrbp1     Ribosome-binding protein 1      Q99PL5  Mmus               2       3
## 3 Iqgap1    Ras GTPase-activating-like pro… Q9JKF1  Mmus               1      13
## 4 Hspa5     78 kDa glucose-regulated prote… P20029  Mmus               1      54
## 5 Pdcd11    Protein RRP5 homolog            Q6NS46  Mmus               1      28

To uniquely identify isoforms, we should consider two keys:

  • the UniProt accession number (named uniprot in both tables)

  • and the isoform number (called isoform and isoform_num respectively)

Because the isoform status was encoded using different names (which is, of course a source of confusion), jdf6 and jdf7 are only automatically joined based on the shared uniprot key.

If the isoform status was encoded the same way in both tables, the join would have been automatically done on both keys!

Here, we need to join using both keys and need to explicitly name the variables used for the join.

inner_join(jdf6, jdf7, by = c("uniprot" = "uniprot", "isoform" = "isoform_num"))
## # A tibble: 2 × 8
##   uniprot organelle         entry isoform gene_name description organism measure
##   <chr>   <chr>             <chr>   <dbl> <chr>     <chr>       <chr>      <dbl>
## 1 Q99PL5  Endoplasmic reti… RRBP…       1 Rrbp1     Ribosome-b… Mmus         102
## 2 Q99PL5  Golgi apparatus   RRBP…       2 Rrbp1     Ribosome-b… Mmus           3

We now see that isoform 1 localised to the ER and has a measured value of 102, while isoform 2, that localised to the GA, has a measured value of 3.

Ideally, the isoform variables should be named identically in the two tables to enable an automatic join with the two keys.

An alternative could be to rename the isoform_num from jdf7 in order to have the both keys names present in both tables, enabling an automatic join. This can be done easily using the rename function from dplyr package.

jdf7 %>% rename(isoform = isoform_num)
## # A tibble: 5 × 6
##   gene_name description                         uniprot organism isoform measure
##   <chr>     <chr>                               <chr>   <chr>      <dbl>   <dbl>
## 1 Rrbp1     Ribosome-binding protein 1          Q99PL5  Mmus           1     102
## 2 Rrbp1     Ribosome-binding protein 1          Q99PL5  Mmus           2       3
## 3 Iqgap1    Ras GTPase-activating-like protein… Q9JKF1  Mmus           1      13
## 4 Hspa5     78 kDa glucose-regulated protein    P20029  Mmus           1      54
## 5 Pdcd11    Protein RRP5 homolog                Q6NS46  Mmus           1      28
inner_join(jdf6, 
           jdf7 %>% 
             rename(isoform = isoform_num)) 
## Joining with `by = join_by(uniprot, isoform)`
## # A tibble: 2 × 8
##   uniprot organelle         entry isoform gene_name description organism measure
##   <chr>   <chr>             <chr>   <dbl> <chr>     <chr>       <chr>      <dbl>
## 1 Q99PL5  Endoplasmic reti… RRBP…       1 Rrbp1     Ribosome-b… Mmus         102
## 2 Q99PL5  Golgi apparatus   RRBP…       2 Rrbp1     Ribosome-b… Mmus           3

6.5 Row and column binding

There are two other important functions in R, rbind and cbind, that can be used to combine two dataframes.

  • cbind can be used to bind two data frames by columns, but both must have the same number of rows.
d2
##   a b
## 1 4 4
## 2 5 5
d3
##   v1 v2 v3
## 1  1  3  5
## 2  2  4  6
cbind(d2, d3)
##   a b v1 v2 v3
## 1 4 4  1  3  5
## 2 5 5  2  4  6
  • rbind, can be used to bind two data frames by rows, but both must have the same number of columns, and the same column names!
d1
##   x y
## 1 1 1
## 2 2 2
## 3 3 3
d2
##   a b
## 1 4 4
## 2 5 5

using rbind(d1, d2) would produce an error because both data frames do not have the same column names (even if they have the same number of columns)

If we change the names of d2, it works!

names(d2) <- names(d1)
d1
##   x y
## 1 1 1
## 2 2 2
## 3 3 3
d2
##   x y
## 1 4 4
## 2 5 5
rbind(d1, d2)
##   x y
## 1 1 1
## 2 2 2
## 3 3 3
## 4 4 4
## 5 5 5

Note that beyond the dimensions and column names that are required to match, the real meaning of rbind is to bind data frames that contain observations for the same set of variables - there is more than only the column names!

Note: rbind and cbind are base R functions. The tidyverse alternatives from the dplyr package are bind_rows and bind_cols and work similarly.

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