[BioC] How to create nested data frames

[lgautier at altern.org]

The data.frame can accommodate the presence of a matrix,
given that the number of rows of the matrix and of the data.frame
are matching.
An instance is created as usual:

m <- matrix(1:20, ncol=2)
dataf <- data.frame(m=m, letter=letters[1:10])


Hoping this helps,



Laurent





> Dear Oleg
>
> Thanks for your help, I have tried, but it seems that method
> indicated works when the 2 matrices have the same length, which it is
> not my case. I cannot contruct the data.frame as you indicated if I
> have different lengths for a and b...
>
> Ana
>>
>>
>>---- Mensaje Original ----
>>De: osklyar at ebi.ac.uk
>>Para: aconesa at ochoa.fib.es
>>Asunto: Re: [BioC] How to create nested data frames
>>Fecha: Thu, 25 Oct 2007 23:42:51 +0100
>>
>>>AFAIK it should be impossible, at least directly: a data.frame is
>>>essentially a list of vectors of equal length. However, a matrix in
>>R is
>>>essentially a vector with dim attributes set. So what you can do is
>>>something like this:
>>>
>>># function that uses such a crazy data.frame, x
>>>f = function(x) {
>>>  a = x$a
>>>  dim(a) = attr(x,"matrixdim")
>>>  b = x$b
>>>  dim(b) = dim(a)
>>>  # use matrices, e.g.
>>>  print(dim(b))
>>>}
>>>
>>>m1 = matrix(runif(10),2,5)
>>>m2 = matrix(runif(10),2,5)
>>>
>>>df = data.frame(a=as.numeric(m1), b=as.numeric(m2))
>>>attr(df, "matrixdim") = dim(m1)
>>>
>>>f(df)
>>>
>>>### should print 2 5 as those are the dimensions of matrices!
>>>> f(df)
>>>[1] 2 5
>>>
>>>indeed!
>>>
>>>Well, you need to consider that when you do as.numeric and when you
>>do
>>>'dim' on a vector - you copy the data! But honestly you can always
>>find
>>>a way to pass another object and a list would be more reasonable as
>>you
>>>do not need to copy data. And although the above example works I
>>cannot
>>>think of a situation where it would be justified to use it, also
>>>data.frames are Slow!
>>>
>>>
>>>-
>>>Dr Oleg Sklyar * EMBL-EBI, Cambridge CB10 1SD, UK * +441223494466
>>>
>>>
>>>On Fri, 2007-10-26 at 00:19 +0200, Ana Conesa wrote:
>>>> Dear List,
>>>>
>>>> This is more an R than a Bioconductor question but I cannot post
>>at
>>>> the R list at the moment, so I apologize for using Bioconductor
>>>> instead.
>>>>
>>>> I am trying to use the pls package to compute pls regression of
>>gene
>>>> expression data on medical variables. I should provide my data as
>>a
>>>> data.frame (NOT A LIST) which contains the matrices of X and Y
>>>> variables, i.e. if mydata is such data frame then mydata$expr
>>gives
>>>> the expression matrix and mydata$medical is the matrix of medical
>>>> data.
>>>> If I do:
>>>> >mydata <- data.frame(expr=expr, medical=medical)
>>>>
>>>> I simply obtain a single data.frame combining the two and I am not
>>>> able to call the matrices independently  I have been seaching the
>>R
>>>> help and documentation without sucess.
>>>> Any help appreciated.
>>>>
>>>> Ana
>>>>
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>>>
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>>ormatics.conductor
>>>
>
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