[R] Output of order() incorrectly ordered?

[Shirley Wu]

Hello,

I have a data frame consisting of four columns and would like to sort  
based on the first column and then write the sorted data frame to a  
file.

 > df <- read.table("file.txt", sep="\t")
where file.txt is simply a tab-delimited file containing 4 columns of  
data (first 2 numeric, second 2 character). I then do,

 > df_ordered <- df[order(df$V1), ]

OR, I assume equivalently,

 > df_ordered <- df[ do.call(order, df), ]

and then,

 > write.table(df_ordered, file="newfile.txt", ...)

The input data file looks like this:

0.083044        375.276 680220  majority
5.50816e-09     2.48914e-05     26377   conformation
0.000169618     0.766505        1546938 interaction
3.90425e-05     0.176433        1655338 vitamin
0.0378182       170.9   1510941 array
3.00359e-07     0.00135732      69421   oligo(dT)-cellulose
1.01517e-13     4.58754e-10     699918  elastase
...

I'd like the output file to look the same except sorted by the first  
column. The output of the commands above give me something that is  
sorted in some places but not sorted in others:

[sorted section]
...
1.87276e-07     0.000846299     1142090 vitamin K
1.89026e-07     0.000854207     917889  leader peptide
1.90884e-07     0.000862605     31206   s
0.00536062      24.2246 1706420 prevent
5.42648e-05     0.245223        1513041 measured
5.42648e-05     0.245223        1513040 measured
0.019939        90.1044 12578   fly
0.00135512      6.12377 61688   GPI
0.00124421      5.62257 681915  content
0.0128271       57.9655 681916  estimated
...
[sorted section]
...
[unsorted section]
...
[etc]

I'm not sure if this is a problem with the input data or with order()  
or what. I am only doing this in R because many of my numeric values  
are expressed in exponential notation and UNIX sort does not handle  
this to my knowledge, but this behavior baffles me. I am pretty new  
to R so it's possible I'm missing something.

Any insight would be greatly appreciated!

Thanks,
-Shirley
graduate student
Stanford University