A    B    C
 1    2    3
 4    5    6

B    C    A
 2    3    1
 5    6    4

mydf <- data.frame(A = 1:2, B = 3:4, C = 5:6)
matches <- data.frame(X = 1:3, Y = c("C", "A", "B"), Z = 4:6)
mydf
#   A B C
# 1 1 3 5
# 2 2 4 6
matches
#   X Y Z
# 1 1 C 4
# 2 2 A 5
# 3 3 B 6

out <- mydf[matches$Y]
out
#   C A B
# 1 5 1 3
# 2 6 2 4

library(data.table)
setDT(mydf)
mydf
#    A B C
# 1: 1 3 5
# 2: 2 4 6

setcolorder(mydf, as.character(matches$Y))
mydf
#    C A B
# 1: 5 1 3
# 2: 6 2 4

df <- read.table(h=T, text="A    B    C
    1    2    3
    4    5    6")
vec <- c("B", "C", "A")
df[vec]

B C A
1 2 3 1
2 5 6 4

df[df.clust$mutation_id]

mydf <- data.frame(A = 1:2, B = 3:4, C = 5:6)
#   A B C
# 1 1 3 5
# 2 2 4 6
matches <- c("B", "C", "A") #desired order

mydf_reorder <- mydf[,match(matches, colnames(mydf))]
colnames(mydf_reorder)
#[1] "B" "C" "A"

match(matches, colnames(mydf))
#[1] 2 3 1