How can I subset a DNAStringSet object by name?

Question

Suppose I have this DNAStringSet (as example)

dataset1

  A DNAStringSet instance of length 38874
        width seq names                  
    [1]  2617 GGC yellow
    [2]  4306 ACG blue
    [3]  1070 CTC red
    [4]  1870 CAC white
    [5]  3732 CAC brown
    ...   ... ...
[38870]   390 TGC black
[38871]  1970 CAG orange

and the I have a vector containing the names of some of these sequences:

dataset2 <- c("blue","black","red","brown")

How can I subset those sequences from dataset1 that have the names in dataset2 ?

Answer 1

DNAStringSet objects can be subset by name just like a normal R list using square bracket notation:

afastafile <- DNAStringSet(c("GCAAATGGG", "CCCGGGTT", "AAAGGGTT", "TTTGGGCC")) 
names(afastafile) <- c("ABC1_1", "ABC2_1", "ABC3_1", "ABC4_1")

afastafile
  A DNAStringSet instance of length 4
    width seq                       names               
[1]     9 GCAAATGGG                 ABC1_1
[2]     8 CCCGGGTT                  ABC2_1
[3]     8 AAAGGGTT                  ABC3_1
[4]     8 TTTGGGCC                  ABC4_1

nms <- c('ABC1_1', 'ABC3_1')
afastafile[nms]

  A DNAStringSet instance of length 2
    width seq                        names               
[1]     9 GCAAATGGG                  ABC1_1
[2]     8 AAAGGGTT                   ABC3_1

In your case, you'd just do dataset1[dataset2]