BCArg BCArg - 3 months ago 25
R Question

R subset a column in data frame based on another data frame/list

I have the following

table1
which is a data frame composed of 6 columns and 8083 rows. Below I am displaying the head of this
table1
:

|gene ID | prom_65| prom_66| amast_69| amast_70| p_value|
|:--------------|---------:|---------:|---------:|---------:|---------:|
|LdBPK_321470.1 | 24.7361| 25.2550| 31.2974| 45.4209| 0.2997430|
|LdBPK_251900.1 | 107.3580| 112.9870| 77.4182| 86.3211| 0.0367792|
|LdBPK_331430.1 | 72.0639| 86.1486| 68.5747| 77.8383| 0.2469355|
|LdBPK_100640.1 | 43.8766| 53.4004| 34.0255| 38.4038| 0.1299948|
|LdBPK_330360.1 | 2382.8700| 1871.9300| 2013.4200| 2482.0600| 0.8466225|
|LdBPK_090870.1 | 49.6488| 53.7134| 59.1175| 66.0931| 0.0843242|


I have another data frame, called
accessions40
which is a list of 510 gene IDs. It is a subset of the first column of
table1
i.e. all of its values (510) are contained in the first column of
table1
(8083). The head of
accessions40
is displayed below:

|V1 |
|:--------------|
|LdBPK_330360.1 |
|LdBPK_283000.1 |
|LdBPK_360210.1 |
|LdBPK_261550.1 |
|LdBPK_367320.1 |
|LdBPK_361420.1 |


What I want to do is the following: I want to produce a new
table2
which contains under the first column (gene ID) only the values present in
accessions40
and the corresponding values from the other five columns from
table1
. In other words, I want to subset the first column of my
table1
based on the values of
accessions40
.

Answer

We can use %in% to get a logical vector and subset the rows of the 'table1' based on that.

subset(table1, gene_ID %in% accessions40$V1)

A better option would be data.table

library(data.table)
setDT(table1)[gene_ID %chin% accessions40$V1]

Or use filter from dplyr

library(dplyr)
table1 %>%
      filter(gene_ID %in% accessions40$V1)