[R] attempted merge() returns: cannot coerce type 'closure' to vector of type 'any'

[Karl Brand]

On 12/2/2010 11:36 AM, David Winsemius wrote:
>
> On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
>
>> Cheers Bill.
>>
>> You got me halfway, since:
>>
>> > temp <- merge(x=x, y=y[,17, drop=FALSE], by="rownames", sort=FALSE)
>> Error in fix.by(by.x, x) : 'by' must specify valid column(s)
>>
>> but, using "row.names" instead of "rownames", like:
>> > temp <- merge(x=x, y=y[,17, drop=FALSE], by="row.names", sort=FALSE)
>>
>> works (but adds a column "Row.names").
>>
>> Which seems some what counter intuitive to me since i am feeding in
>> two matrices to the merge function, which i understand have
>> 'rownames', not 'row.names' as data frames have, right? Although the
>> output of merge() is a data frame...
>>
>
> This reminds me of physicists using high energy particles to investigate
> the structure of the nucleus. But you have alternatives to what might be
> called "destructive debugging through binoculars". Instead of throwing
> code at your data and asking the assembled audience of soothsayers to
> tell you what went wrong by examining the debris, why don't you show us
> what the data objects actually look like?
>

Ofcourse David, sorry- my lazy.

Is str() enough to put away the binoculuars and maybe highlight the 
source of my ignorance?

 > str(x)
  num [1:140, 1:7] 4.93e-02 2.83e-02 1.07e-02 2.68e-02 3.92e-05 ...
  - attr(*, "dimnames")=List of 2
   ..$ : chr [1:140] "1415743_at" "1415887_at" "1416332_at" 
"1416340_a_at" ...
   ..$ : chr [1:7] "R.S.adj.pvalue" "R.S.Tau" "R.S.xpiek" "R.S.xdal" ...

 > str(y)
  num [1:140, 1:18] 0.573 1 0.752 0.768 0.399 ...
  - attr(*, "dimnames")=List of 2
   ..$ : chr [1:140] "1427982_s_at" "1430520_at" "1454086_a_at" 
"1419652_s_at" ...
   ..$ : chr [1:18] "R.S.1" "R.S.2" "R.S.3" "R.S.4" ...
 > source(.trPaths[5], echo=TRUE, max.deparse.length=150)

 > str(temp)
'data.frame':   140 obs. of  9 variables:
  $ Row.names     :Class 'AsIs'  chr [1:140] "1415743_at" "1415887_at" 
"1416332_at" "1416340_a_at" ...
  $ R.S.adj.pvalue: num  4.93e-02 2.83e-02 1.07e-02 2.68e-02 3.92e-05 ...
  $ R.S.Tau       : num  21.6 23.6 26.6 29.7 18.8 20 24.6 27.9 23.9 22.7 ...
  $ R.S.xpiek     : num  6.74 17.46 15.81 15.39 14.73 ...
  $ R.S.xdal      : num  16.94 1.76 22.8 1.12 5.41 ...
  $ R.S.p1        : num  0.0004 0.0001 0.0467 0.0024 0 ...
  $ R.S.p2        : num  0.0039 0 0.002 0.019 0.0001 0.0035 0.0351 
0.0126 0.0028 0.0192 ...
  $ R.S.p3        : num  0.0178 0.0004 0.0101 0.0312 0.0012 0.022 0.0008 
0.0151 0.0048 0.0317 ...
  $ V1            : num  3.96 -0.94 1.04 1.94 -2.53 ...
 >




-- 
Karl Brand <k.brand at erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3211 | F +31 (0)10 704 4743 | M +31 (0)642 777 268