On 28.10.2012 10:32, Benjamin Ward (ENV) wrote:
Hi All,
I'm trying to run a simulation of host-pathogen evolution based around
individuals.
What I need to have is a dataframe or table of some description - describing
all the individuals of a pathogen population (so far I've implemented this as a
matrix):
ID No_of_Effectors Effectors (Sequences)
[1,] 0001 3 ## 3 Random Numbers ##
There will be many such rows for many individuals. They have something called
effectors, the number of which is randomly generated, so say you get 3 in the
No_of_Effectors column. Then I make R generate 3 numbers from between 1 and
10,000, this gives me three numerical representations of genes. These numbers
will be compared to a similar data structure of the host individuals who have
their immune genes with similar numbers.
My problem is that obviously I can't stick 3 numbers in one "cell" of the
matrix (I've tried) :
Pathogen_Individuals[1,3] <- c(2,3,4)
Consider to use a data.frame with the third column (Effectors) of list
type. Then you can do:
Pathogen_Individuals$Effectors[1] <- list(c(2,3,4))
And what you get is:
> Pathogen_Individuals
ID No_of_Effectors Effectors
1 0001 3 2, 3, 4
Uwe Ligges
Error in Pathogen_Individuals[1, 3] <- c(345, 567, 678) :
number of items to replace is not a multiple of replacement length
In future I'm also going to have more variables such as whether a gene is
expressed. Such information may require a matrix in itself - something like:
Effector ID Sequence Expressed?
[1,] 0001 345,567,678 1 (or 0).
Is there a way then I can put more than one value in the cell like a list of values, or a
way to put objects in a cell of a data frame, matrix or table etc. Almost an inception
deal - data structures nested in a data structure? If I search for things like
"insert list into matrix" I get results like how to turn one into another,
which is not what I think I need to be doing.
I have been considering having several data structures not nested in each
other, something like for every individual create a new matrix object with the
name Effectors_[Individual_ID] and some how get my simulation loops operating
on those objects but I find it hard to see how to tell R all of those matrices
are to be included in an operation, as you can all lines of a data frame for
example with for loops.
This is strange for me because this model was written in a macro-code for
another program which handles data in a different format and layout to R.
My problem is I think, each individual in the model has many variables - in
this case representations of genes. So I'm having trouble getting my head about
this.
Hopefully someone more experienced will be able to offer advice or a solution,
it will be very appreciated.
Many Thanks,
Ben Ward (ENV, UEA & The Sainsbury Lab, JIC).
P.S. I have searched previous queries to the list, and I'm not sure but this
may be useful for relevant:
Have you thought of using a list?
a <- matrix(1:10, nrow=2)
b <- 1:5
x <- list(a=a, b=b)
x
$a
[,1] [,2] [,3] [,4] [,5]
[1,] 1 3 5 7 9
[2,] 2 4 6 8 10
$b
[1] 1 2 3 4 5
x$a
[,1] [,2] [,3] [,4] [,5]
[1,] 1 3 5 7 9
[2,] 2 4 6 8 10
x$b
[1] 1 2 3 4 5
oliveoil and yarn datasets have been mentioned.
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and provide commented, minimal, self-contained, reproducible code.
