Re: [R] Output of order() incorrectly ordered?

From: Charles C. Berry <cberry_at_tajo.ucsd.edu>
Date: Tue, 25 Mar 2008 10:03:50 -0700

On Mon, 24 Mar 2008, Shirley Wu wrote:

> 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!

I suspect that the first column contains something that cannot be rendered as a numeric value. Probably you have leading blanks before some of the numbers.

The result is that the first column is a factor, which will be ordered according to the character collating sequence in your locale after coercing it to character. (I am guessing here, but it appears to do this on my PC.)

Try

df <- read.table("file.txt", sep="\t", strip.white=TRUE )

and see if the ordering agrees with your intuition.

HTH, Chuck

>
> Thanks,
> -Shirley
> graduate student
> Stanford University
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry_at_tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

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