[R] unqiue problem

[David Winsemius]

On Jun 14, 2010, at 1:10 PM, David Winsemius wrote:

>
> On Jun 14, 2010, at 12:32 PM, Assa Yeroslaviz wrote:
>
>> I thought unique delete the whole line.
>> I don't really need the row names, but I thought of it as a way of  
>> getting
>> the unique items.
>>
>> Is there a way of deleting whole lines completely according to their
>> identifiers?
>>
>> What I really need are unique values on the first column.
>>
>> Assa
>>
>> On Mon, Jun 14, 2010 at 18:04, jim holtman <jholtman at gmail.com>  
>> wrote:
>>
>>> Your process does remove all the duplicate entries based on the
>>> content of the two columns.  After you do this, there are still
>>> duplicate entries in the first column that you are trying to use as
>>> rownames and therefore the error.  Why to you want to use non-unique
>>> entries as rownames?  Do you really need the row names, or should  
>>> you
>>> only be keeping unique values for the first column?
>>>
>>> On Mon, Jun 14, 2010 at 8:54 AM, Assa Yeroslaviz  
>>> <frymor at gmail.com> wrote:
>>>> Hello everybody,
>>>>
>>>> I have a a matrix of 2 columns and over 27k rows.
>>>> some of the rows are double , so I tried to remove them with the  
>>>> command
>>>> unique():
>>>>
>>>>> Workbook5 <- read.delim(file =  "Workbook5.txt")
>>>>> dim(Workbook5)
>>>> [1] 27748     2
>>>>> Workbook5 <- unique(Workbook5)
>
> Jim already showed you one way in another thread and it is probably  
> more intuitive than this way, but just so you know...
>
> Workbook5 <- Workbook5[ unique(Workbook5[ ,1] ) , ]
>
> ... should have worked. Logical indexing on first column with return  
> of both columns of qualifying rows.

Actually I was thinking a bit askew although that would have  
succeeded. That was not logical indexing, which would have been done  
with duplicated() ... or rather its negation through the use of the  
"!" unary operator:

 > str(unique(Workbook5[ ,1] ) )
  Factor w/ 17209 levels "A_51_P100034",..: 1 2 3 4 5 6 7 8 9 10 ...
 > str(!duplicated(Workbook5[ ,1] ) )
  logi [1:20101] TRUE TRUE TRUE TRUE TRUE TRUE ...

So this would have been the way to do it with logical indexing:

Workbook5 <- Workbook5[ !duplicated(Workbook5[ ,1] ) , ]


>
> -- 
> David.
>>>>> dim(Workbook5)
>>>> [1] 20101     2
>>>>
>>>> it removed a lot of line, but unfortunately not all of them. I  
>>>> wanted to
>>> add
>>>> the row names to the matrix and got this error message:
>>>>> rownames(Workbook5) <- Workbook5[,1]
>>>> Error in `row.names<-.data.frame`(`*tmp*`, value = c(1L, 2L, 3L,  
>>>> 4L, 5L,
>>> :
>>>> duplicate 'row.names' are not allowed
>>>> In addition: Warning message:
>>>> non-unique values when setting 'row.names': ‘A_51_P102339’,
>>>> ‘A_51_P102518’, ‘A_51_P103435’, ‘A_51_P103465’,
>>>> ‘A_51_P103594’, ‘A_51_P104409’, ‘A_51_P104718’,
>>>> ‘A_51_P105869’, ‘A_51_P106428’, ‘A_51_P106799’,
>>>> ‘A_51_P107176’, ‘A_51_P107959’, ‘A_51_P108767’,
>>>> ‘A_51_P109258’, ‘A_51_P109708’, ‘A_51_P110341’,
>>>> ‘A_51_P111757’, ‘A_51_P112427’, ‘A_51_P112662’,
>>>> ‘A_51_P113672’, ‘A_51_P115018’, ‘A_51_P116496’,
>>>> ‘A_51_P116636’, ‘A_51_P117666’, ‘A_51_P118132’,
>>>> ‘A_51_P118168’, ‘A_51_P118400’, ‘A_51_P118506’,
>>>> ‘A_51_P119315’, ‘A_51_P120093’, ‘A_51_P120305’,
>>>> ‘A_51_P120738’, ‘A_51_P120785’, ‘A_51_P121134’,
>>>> ‘A_51_P121359’, ‘A_51_P121412’, ‘A_51_P121652’,
>>>> ‘A_51_P121724’, ‘A_51_P121829’, ‘A_51_P122141’,
>>>> ‘A_51_P122964’, ‘A_51_P123422’, ‘A_51_P123895’,
>>>> ‘A_51_P124008’, ‘A_51_P124719’, ‘A_51_P125648’,
>>>> ‚ÄòA_51_P125679‚Äô, ‚ÄòA_51_P125779‚ [... truncated]
>>>>
>>>> Is there a better way to discard the duplicataions in the text file
>>> (Excel
>>>> file is the origin).
>>>>
>>>>> R.version
>>>>             _
>>>> platform       x86_64-apple-darwin9.8.0
>>>> arch           x86_64
>>>> os             darwin9.8.0
>>>> system         x86_64, darwin9.8.0
>>>> status         Patched
>>>> major          2
>>>> minor          11.1
>>>> year           2010
>>>> month          06
>>>> day            03
>>>> svn rev        52201
>>>> language       R
>>>> version.string R version 2.11.1 Patched (2010-06-03 r52201)
>>>>
>>>> THX
>>>>
>>>> Assa
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list

David Winsemius, MD
West Hartford, CT