[R] Having some Trouble Data Structures

[arun]

HI,
May be this helps. 

dat1<-data.frame(ID=formatC(0001:0010,width=4,flag="0"),No_of_Effectors=rep(3,10))
dat1<-within(dat1,{ID<-as.character(ID)})
list1<-lapply(1:nrow(dat1),function(x) paste(sample(1:10000,3,replace=TRUE)),sep=",")

dat2<-data.frame(dat1,do.call(rbind,lapply(lapply(1:nrow(dat1),function(x) sample(1:10000,3,replace=TRUE)),function(x) paste(x,collapse=","))))
colnames(dat2)[3]<-"Effectors"
 dat2
#     ID No_of_Effectors      Effectors
#1  0001               3 4759,8109,7997
#2  0002               3 2649,9496,9167
#3  0003               3 4229,3282,6235
#4  0004               3 5388,3088,6420
#5  0005               3 5602,5981,4749
#6  0006               3 4971,6956,5913
#7  0007               3  4999,9465,799
#8  0008               3  8419,4346,266
#9  0009               3 9329,8819,4011
#10 0010               3 5817,8729,6499
 dat3<-within(dat2,{Effectors<-as.character(Effectors)})

#converting back the Effector column to numeric 3 columns
res<-do.call(rbind,lapply(strsplit(dat3[,3],","),function(x) as.numeric(x)))
 head(res)
#     [,1] [,2] [,3]
#[1,] 4759 8109 7997
#[2,] 2649 9496 9167
#[3,] 4229 3282 6235
#[4,] 5388 3088 6420
#[5,] 5602 5981 4749
#[6,] 4971 6956 5913


A.K.





----- Original Message -----
From: Benjamin Ward (ENV) <B.Ward at uea.ac.uk>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Sunday, October 28, 2012 5:32 AM
Subject: [R] Having some Trouble Data Structures

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)
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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