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

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...

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?

On 12/2/2010 11:36 AM, David Winsemius wrote:

On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:

Cheers Bill.

I don't understand why i get this error message when attempting to  
use merge() -

temp <- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE)

Error in as.vector(x, mode) :
 cannot coerce type 'closure' to vector of type 'any'

Try
   by="rownames"
instead of
   by=rownames

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...

On Dec 2, 2010, at 5:58 AM, Karl Brand wrote:

On 12/2/2010 11:36 AM, David Winsemius wrote:

On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:

Cheers Bill.

Inserting earlier debris:

I don't understand why i get this error message when attempting to
use merge() -

temp <- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE)

Error in as.vector(x, mode) :
cannot coerce type 'closure' to vector of type 'any'

Try
by="rownames"
instead of
by=rownames

At this point I think Bill should have suggested by="row.names" since
that is the correct argument to merge() when asking for a rownames
match, and you appear to have found that by experimentation since you
didn't seem to have read the help page.

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").

OK. It added a column what's the problem? The help(merge) pages says:
"If the matching involved row names, an extra character column called
Row.names is added at the left, and in all cases the result has
?automatic? 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...

Right. The merge function takes either dataframes or things which can be
coerced to dataframes as arguments and returns a dataframe. That is
exactly what the help(merge) page states outright (in many places). Just
because your arguments were matrices doesn't mean the returned object
should be one. Had you wanted it to be an "augmented" data.matrix with
rownames as before, you could gotten that after merge by:

?data.matrix
temp2 <- datamatrix(temp[-1])
rownames(temp2) <- temp$Row.names

(Or by the rather nice manipulations that you described using rownames
as indices.)

I think I understand the "problem" now .... that you were expecting
merge() to behave differently than is documented.

-----Original Message-----
From: Karl Brand [mailto:k.brand at erasmusmc.nl] 
Sent: Thursday, December 02, 2010 2:22 AM
To: William Dunlap
Cc: r-help at r-project.org; Dimitris Rizopoulos
Subject: Re: [R] attempted merge() returns: cannot coerce 
type 'closure' to vector of type 'any'

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...

thanks again,

Karl


On 12/1/2010 6:08 PM, William Dunlap wrote:

Try
    by="rownames"
instead of
    by=rownames

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

-----Original Message-----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Karl Brand
Sent: Wednesday, December 01, 2010 6:35 AM
To: Dimitris Rizopoulos
Cc: r-help at r-project.org
Subject: [R] attempted merge() returns: cannot coerce type
'closure' to vector of type 'any'

Hi Dimtris and esteemed useRs,

I don't understand why i get this error message when
attempting to use
merge() -

  >  temp<- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE)

Error in as.vector(x, mode) :
    cannot coerce type 'closure' to vector of type 'any'

It should work because:

  >  all(rownames(x[order(rownames(x)),]) ==

+ rownames(y[order(rownames(y[,17, drop=FALSE])),17,
drop=FALSE]) ....
[TRUNCATED]
[1] TRUE

also:

  >  class(x); class(y[,17, drop=FALSE])

[1] "matrix"
[1] "matrix"


Any idea why i cant use merge() in the normal way here? 

I'm forced to

add the column using:

temp.b<- cbind(x, y[match(rownames(x), rownames(y)),17])

All insights appreciated for this leaRner,

cheers,

Karl


--
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

-- 
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

I didn't change your "rownames" to "row.names"
because I figured you had the name you wanted
but only forgot to include the quotes.  Both "rownames"
and "row.names" are valid inputs, but they mean
different things.  Howver, without the quotes you were
passing in the contents of the object called
rownames, which happens to be a function (aka a closure),
not the string "rownames.  The quotes are needed to
distinguish between things and names of things.
Some functions (e.g., library() and help()) try
to cover up this difference, leading to occasional
difficulties using them.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

-----Original Message-----
From: Karl Brand [mailto:k.brand at erasmusmc.nl]
Sent: Thursday, December 02, 2010 2:22 AM
To: William Dunlap
Cc: r-help at r-project.org; Dimitris Rizopoulos
Subject: Re: [R] attempted merge() returns: cannot coerce
type 'closure' to vector of type 'any'

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...

thanks again,

Karl


On 12/1/2010 6:08 PM, William Dunlap wrote:

Try
     by="rownames"
instead of
     by=rownames

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

-----Original Message-----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Karl Brand
Sent: Wednesday, December 01, 2010 6:35 AM
To: Dimitris Rizopoulos
Cc: r-help at r-project.org
Subject: [R] attempted merge() returns: cannot coerce type
'closure' to vector of type 'any'

Hi Dimtris and esteemed useRs,

I don't understand why i get this error message when
attempting to use
merge() -

   >   temp<- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE)

Error in as.vector(x, mode) :
     cannot coerce type 'closure' to vector of type 'any'

It should work because:

   >   all(rownames(x[order(rownames(x)),]) ==

+ rownames(y[order(rownames(y[,17, drop=FALSE])),17,
drop=FALSE]) ....
[TRUNCATED]
[1] TRUE

also:

   >   class(x); class(y[,17, drop=FALSE])

[1] "matrix"
[1] "matrix"


Any idea why i cant use merge() in the normal way here?

I'm forced to

add the column using:

temp.b<- cbind(x, y[match(rownames(x), rownames(y)),17])

All insights appreciated for this leaRner,

cheers,

Karl


--
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

--
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