I have the following dataset. I want to sort it by second column.

dat <- read.table(header=TRUE, text="
                  ID  LFrom LTo It1 It2 It3 It4
                  ab7    1   2   47  152 259 140
                  ab8   1.1   2.1   88  236 251 145
                  ab21   1.2   2.1  72  263 331 147
                  ab3    1   2   71  207 290 242
                  ab300    1   2   47  152 259 140
                  ab4    1.2   2.1  72  263 331 147
                  ab10    1.1   2   71  207 290 242
                  ab501    1   2   47  152 259 140
                  ")

dat
     ID LFrom LTo It1 It2 It3 It4
1   ab7   1.0 2.0  47 152 259 140
2   ab8   1.1 2.1  88 236 251 145
3  ab21   1.2 2.1  72 263 331 147
4   ab3   1.0 2.0  71 207 290 242
5 ab300   1.0 2.0  47 152 259 140
6   ab4   1.2 2.1  72 263 331 147
7  ab10   1.1 2.0  71 207 290 242
8 ab501   1.0 2.0  47 152 259 140

By using the following code, I find:

dat[with(dat, order(LFrom, ID)),]
     ID LFrom LTo It1 It2 It3 It4
4   ab3   1.0 2.0  71 207 290 242
5 ab300   1.0 2.0  47 152 259 140
8 ab501   1.0 2.0  47 152 259 140
1   ab7   1.0 2.0  47 152 259 140
7  ab10   1.1 2.0  71 207 290 242
2   ab8   1.1 2.1  88 236 251 145
3  ab21   1.2 2.1  72 263 331 147
6   ab4   1.2 2.1  72 263 331 147

The sorting in ID is not really sorted according to the number value. I rewrite the data by putting extra 00 and 0 (manually) like the following:

dat1 <- read.table(header=TRUE, text="
                  ID  LFrom LTo It1 It2 It3 It4
                  ab007    1   2   47  152 259 140
                  ab008   1.1   2.1   88  236 251 145
                  ab021   1.2   2.1  72  263 331 147
                  ab003    1   2   71  207 290 242
                  ab300    1   2   47  152 259 140
                  ab004    1.2   2.1  72  263 331 147
                  ab010    1.1   2   71  207 290 242
                  ab501    1   2   47  152 259 140
                  ")
dat1
     ID LFrom LTo It1 It2 It3 It4
1 ab007   1.0 2.0  47 152 259 140
2 ab008   1.1 2.1  88 236 251 145
3 ab021   1.2 2.1  72 263 331 147
4 ab003   1.0 2.0  71 207 290 242
5 ab300   1.0 2.0  47 152 259 140
6 ab004   1.2 2.1  72 263 331 147
7 ab010   1.1 2.0  71 207 290 242
8 ab501   1.0 2.0  47 152 259 140

Now the following code works fine:

dat1[with(dat1, order(LFrom, ID)), ]
     ID LFrom LTo It1 It2 It3 It4
4 ab003   1.0 2.0  71 207 290 242
1 ab007   1.0 2.0  47 152 259 140
5 ab300   1.0 2.0  47 152 259 140
8 ab501   1.0 2.0  47 152 259 140
2 ab008   1.1 2.1  88 236 251 145
7 ab010   1.1 2.0  71 207 290 242
6 ab004   1.2 2.1  72 263 331 147
3 ab021   1.2 2.1  72 263 331 147

I have a large list of dataset. Manually changing the ID is tough. All I need to get the ID sorted (with including 00 and 0).

You can change the with a combination of substr and sprintf as follows:

dat$ID <- paste0(substr(dat$ID,1,2),sprintf("%03d",as.numeric(substr(dat$ID,3,5))))

this gives:

> dat[with(dat, order(LFrom, ID)), ]
     ID LFrom LTo It1 It2 It3 It4
4 ab003   1.0 2.0  71 207 290 242
1 ab007   1.0 2.0  47 152 259 140
5 ab300   1.0 2.0  47 152 259 140
8 ab501   1.0 2.0  47 152 259 140
2 ab008   1.1 2.1  88 236 251 145
7 ab010   1.1 2.0  71 207 290 242
6 ab004   1.2 2.1  72 263 331 147
3 ab021   1.2 2.1  72 263 331 147