[R] Looping over groups

[Peter Dalgaard]

Dylan Beaudette wrote:
> On Wed, Aug 20, 2008 at 7:48 AM, Josh B <joshb41 at yahoo.com> wrote:
>   
>> Hello,
>>
>> My R skills are somewhere between novice and intermediary, and I am hoping that some of you very helpful forum members, whom I've seen work your magic on other peoples' problems/questions, can help me here.
>>
>> I have a matrix with the following format:
>>
>> (i) individual plants comprising many different genotype groups (i.e., a plant is genotype 1 or genotype 2 or genotype 3, etc). The column for genotypes is called "gen", and the plants are members of genotype class 1 - 309, with no overlaps (i.e., you're either a genotype 1 or a genotype something else, but not both) and no missing values.
>> (ii) Various trait measurements taken on the plants, with multiple replicates per genotype group
>>
>> I want to create a covariance matrix, separately for plants from each genotype group. I know how to use the command "cov"; my problem is that I have 309 different genotype groups and so I need to set up some sort of an automated loop to go through each genotype group and create a separate covariance matrix based on it.
>>
>> My question is, how do I make a loop to automatically go through and create these covariance matrices, i.e., a separate covariance matrix for plants from each genotype group?
>>
>> I am familiar with the "for" command, but I cannot get it to work. Here is my code:
>>
>> christina= read.table("christina.txt", sep= ",", na= "NA", header= TRUE)
>> {for (i in 1:309)
>> christina.i= subset(christina, gen == i)
>> christina.i.clean= christina.i[,-1]
>> christina.matrix.i= as.matrix(christina.i.clean)
>> christina.cov.i= cov(christina.matrix.i, y= NULL, use= "complete.obs", method= c("pearson"))
>> write.table(christina.cov.i, sep= ",", file= "covariances.csv", row.names= FALSE, col.names= FALSE, append= TRUE)}
>>
>>
>> The problem occurs at my code snippet "gen == i". I want R to insert a number in place of "i", depending on what round of the loop it is on, but R insists that I am literally referring to a genotype class named "i". I have made sure that the column "gen" is numeric, but the same problem persists if I make the column a factor instead.
>>
>> Any help would be much appreciated, but help that includes sample code would be most useful. Thank you in advance!
>>
>> Sincerely,
>> Josh
>>
>>     
>
> If you can make your data into a dataframe, you can use something like this:
>
> # might work
> christina.df <- as.data.frame(christina)
>
> # this should work, if your ID var ('gen') is the first column in the data frame
> by(christina.df, christina.df$gen, function(d) {
> d.clean <- d[,-1]
> cov(d.clean, y= NULL, use= "complete.obs", method= c("pearson")
> } )
>
> for more ideas, see ?by
>
>   
also

dd <- christina ## just for brevity
lapply(split(dd[-1], dd[1]), cov, use="complete.obs")



-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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