error: unused argument (nomatch = 0) when using data.table indexing

Question

I am trying to use the data.table index to perform a fast lookup.

table = c("AX-11415458", "AX-11417054", "AX-11419082", "AX-11421703", 
"AX-11422856", "AX-11422870")

df1 = structure(list(V1 = c(26L, 26L, 26L, 26L, 26L, 26L), V2 = c("AX-11415458", 
"AX-11417054", "AX-11419082", "AX-11421703", "AX-11422856", "AX-11422870"
), V3 = c(0L, 0L, 0L, 0L, 0L, 0L), V4 = c(705L, 3973L, 2859L, 
1683L, 6482L, 11930L), V5 = c("C", "G", "C", "A", "C", "G"), 
    V6 = c("A", "A", "T", "G", "T", "T")), row.names = c(NA, 
-6L), class = "data.frame")

df2=structure(list(V1 = c("MT", "MT", "MT", "MT", "MT", "MT"), V2 = c("AX-11415458", 
"AX-11417054", "AX-11419082", "AX-11421703", "AX-11422856", "AX-11422870"
), V3 = c(0L, 0L, 0L, 0L, 0L, 0L), V4 = c(705L, 3973L, 2859L, 
1683L, 6482L, 11930L), V5 = c(".", ".", ".", ".", ".", "."), 
    V6 = c("A", "A", "T", "G", "T", "T")), row.names = c(NA, 
-6L), class = "data.frame")

setDT(df1)
setDT(df2)

setkey(df1, V2)
setkey(df2, V2)

I would like to iterate over table and lookup the value in both df1 and df2 and replace V5 and V6 in df2 with those in df1.

for (i in table) {
    df2[.(i), nomatch = 0L][,5:6] = df1[.(i), nomatch = 0L][,5:6]
}

But I get the error:

Error in [<-.data.table ( *tmp* , .(i), nomatch = 0L, value = list(V1 = "MT", : unused argument (nomatch = 0)

Why can't I do this and is there a correct way to do what I want?

Answer 1

In fact, yours can be directly corrected as

for (i in table) {
  df2[i,5:6] <- df1[i,5:6]
}

nomatch = 0L is only used for inner join and the chain [,5:6] will not update the data in original df .

In addition, You can also try this method

setDT(df1)
setDT(df2)
df3 <- df1[V2 %chin% table]
setkey(df2,V2)
setkey(df3,V2)
df2[,`:=`(
  V5=fcoalesce(df3[df2,V5]),
  V6=fcoalesce(df3[df2,V6])
  )
  ]

Result

> df2

   V1          V2 V3    V4 V5 V6
1: MT AX-11415458  0   705  C  A
2: MT AX-11417054  0  3973  G  A
3: MT AX-11419082  0  2859  C  T
4: MT AX-11421703  0  1683  A  G
5: MT AX-11422856  0  6482  C  T
6: MT AX-11422870  0 11930  G  T