[R] Having some Trouble Data Structures
arun
smartpink111 at yahoo.com
Sun Oct 28 16:38:15 CET 2012
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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