Hello, my question is fairly simple but I still cannot get the correct synthax. I would like to move one member of the DNA String Set to the top of the Set, such as:

Original:

 A DNAStringSet instance of length 10
     width seq                                                                                             names               
 [1] 100 ----------------------------------------------...---------------------------------------------- gene_5
 [2] 100 ----------------------------------------------...---------------------------------------------- gene_3
 [3] 100 ----------------------------------------------...---------------------------------------------- gene_1
 [4] 100 ----------------------------------------------...---------------------------------------------- gene_9

Target:

A DNAStringSet instance of length 10
     width seq                                                                                             names               
 [1] 100 ----------------------------------------------...---------------------------------------------- gene_1
 [2] 100 ----------------------------------------------...---------------------------------------------- gene_5
 [3] 100 ----------------------------------------------...---------------------------------------------- gene_3
 [4] 100 ----------------------------------------------...---------------------------------------------- gene_9

Do it the same way you would do it with a character vector or any vector-like object:

library(Biostrings)
x <- DNAStringSet(c(a="TATCA", b="GGGGGCCC", c="AA", d="CAGAGCA"))
x
#   A DNAStringSet instance of length 4
#     width seq                                               names               
# [1]     5 TATCA                                             a
# [2]     8 GGGGGCCC                                          b
# [3]     2 AA                                                c
# [4]     7 CAGAGCA                                           d

Move 3rd element to the top:

c(x[3], x[-3])
#   A DNAStringSet instance of length 4
#     width seq                                               names               
# [1]     2 AA                                                c
# [2]     5 TATCA                                             a
# [3]     8 GGGGGCCC                                          b
# [4]     7 CAGAGCA                                           d

More generally:

moveToTop <- function(x, n) c(x[n], x[-n])

moveToTop(x, 4)
#   A DNAStringSet instance of length 4
#     width seq                                               names               
# [1]     7 CAGAGCA                                           d
# [2]     5 TATCA                                             a
# [3]     8 GGGGGCCC                                          b
# [4]     2 AA                                                c

moveToTop(x, 1)  # no-op
#   A DNAStringSet instance of length 4
#     width seq                                               names               
# [1]     5 TATCA                                             a
# [2]     8 GGGGGCCC                                          b
# [3]     2 AA                                                c
# [4]     7 CAGAGCA                                           d

Also works for moving more than one element to the top:

moveToTop(x, c(4, 2))
#   A DNAStringSet instance of length 4
#     width seq                                               names               
# [1]     7 CAGAGCA                                           d
# [2]     8 GGGGGCCC                                          b
# [3]     5 TATCA                                             a
# [4]     2 AA                                                c

Works on any vector-like object:

moveToTop(101:110, c(5, 2, 4))
#  [1] 105 102 104 101 103 106 107 108 109 110

Hope this helps,

H.