R: subsetting dataframe using elements from a vector

Question

I have a data frame which includes a vector of individual identifiers (which are 6 letters) and vectors of numbers

I would like to subset it using a vector of elements (again 6-letters identifiers) taken from another dataframe

Here is what I did (in a simplified version, my dataframe has over 200 columns and 64 rows)

n = c(2, 3, 5, 7, 8, 1) 

i = c("abazzz", "bbaxxx", "ccbeee","dddfre", "sdtyuo", "loatvz" ) 

c = c(10, 2, 10, 2, 12, 34) 

df1 = data.frame(n, i, c) 

attach(example)

This is the vector whose elements I want to use for subsetting:

v<- c("abazzz", "ccbeee", "lllaaa")

This is what I do to subset

df2<-example[, i==abazzz | ccbeee | lllaaa]

This does not work, the error I get is "abazzz" not found ( I tried with and without "", I tried using the command subset, same error appears)

Moreover I would like to avoid the or operator as the vector I need to use for subsetting has about 50 elements. So, in words, what I would like to do is to subset df2 in order to extract only those individuals who already appear in df1 using their identifiers (column in df1)

Writing this makes me think this must be very easy to do, but I can't figure it out by myself, I tried looking up similar questions but could not find what I was looking for. I hope someone can help me, suggest other posts or manuals so I can learn. Thanks!

You have to use quotes "abazzz", Please don't attach the dataset.. Use %in% ie. df1[df1$i %in% v,] — akrun
– akrun, Commented Jan 8, 2015 at 10:27

David Arenburg · Accepted Answer · 2015-01-09 11:31:27Z

3

Here's another nice option using data.tables binary search (for efficiency)

library(data.table)
setkey(setDT(df1), i)[J(v), nomatch = 0]
#    n      i  c
# 1: 2 abazzz 10
# 2: 5 ccbeee 10

Or if you don't want to reorder the data set and keep the syntax similar to base R, you could set a secondary key instead (contributed by @Arun)

set2key(setDT(df1), i) 
df1[i %in% v]

Or dplyr (for simplicity)

library(dplyr)
df1 %>% filter(i %in% v)
#    n      i  c
# 1: 2 abazzz 10
# 2: 5 ccbeee 10

As a side note: as mentioned in comments, never use attach

edited Jan 9, 2015 at 11:31

answered Jan 8, 2015 at 10:38

David Arenburg

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Comments

lukeA · Accepted Answer · 2015-01-08 10:29:28Z

2

(1) Instead of

attach(df1)
df2<-df1[, i==abazzz | ccbeee | lllaaa]
detach(df1)

try

df2 <- with(df1, df1[i=="abazzz" | i=="ccbeee" | i=="lllaaa", ])

(2)

with(df1, df1[i %in% v, ])

Both yield

#   n      i  c
# 1 2 abazzz 10
# 3 5 ccbeee 10

answered Jan 8, 2015 at 10:29

lukeA

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