[R] How to match strings in two files and replace strings?

[Ana Marija]

I have a file like this: (has 308545 lines)

    head output11.frq
     CHR               SNP   A1   A2          MAF  NCHROBS
       1      1:775852:T:C    T    C       0.1707     3444
       1     1:1120590:A:C    C    A      0.08753     3496
       1     1:1145994:T:C    C    T       0.1765     3496
       1     1:1148494:A:G    A    G       0.1059     3464
       1     1:1201155:C:T    T    C      0.07923     3496
    ...

And another file (marker-info) which has the first 24 commented lines
and is comma separated that looks like this (has total of 500593
lines):

    1,742429,SNP_A-1909444,ss66079302,rs3094315,36.2,G,A,C,T,A,GCACAGCAAGAGAAAC[A/G]TTTGACAGAGAATACA,Sty,+,-,y,,,127,phs000018
    1,769185,SNP_A-4303947,ss66273559,rs4040617,36.2,A,G,A,G,A,GCTGTGAGAGAGAACA[A/G]TGTCCCAATTTTGCCC,Sty,+,+,n,,,127,phs000018
    1,775852,SNP_A-1886933,ss66317030,rs2980300,36.2,T,C,A,G,A,GAATGACTGTGTCTCT[C/T]TGAGTTAGTGAAGTCA,Nsp,-,+,y,,,127,phs000018
    1,782343,SNP_A-2236359,ss66185183,rs2905036,36.2,C,T,C,T,A,CTCGATTTGTGTTCAA[C/T]ATATTTCATTTGTACC,Sty,-,-,n,,,127,phs000018
    1,1201155,SNP_A-2205441,ss66174584,rs4245756,36.2,C,T,C,T,A,CCAGTGCTTTCAACCA[C/T]ACTCACTTTTCACTGT,Sty,+,+,n,,,127,phs000018
    ...

I want to replace in output11.frq second column with the 5th column in
marker-info that has the matching value in 1st and 2nd column so for
this example the result of the output11.frq would look like this:

    1      rs2980300    T    C       0.1707     3444
    1      rs4245756    T    C      0.07923     3496

I tried doing this in bash but I got empty file:

    vi tst.awk
    NR==FNR { map[$1,$2]=$5; next }
    ($1,$4) in map { $2=map[$1,$4]; print }
    awk -f tst.awk FS=',' marker-info FS='\t' output11.frq  > output11X.frq

Can this be done in R?

Thanks
Ana