2008/8/20 Josh B <[EMAIL PROTECTED]>:
> Here is my underlying data file. Of course, please don't feel obliged to
> spend any more time on this!
>
>
> ----- Original Message ----
> From: Dylan Beaudette <[EMAIL PROTECTED]>
> To: Josh B <[EMAIL PROTECTED]>
> Cc: r-help@r-project.org
> Sent: Wednesday, August 20, 2008 10:58:26 AM
> Subject: Re: [R] Looping over groups
>
> On Wed, Aug 20, 2008 at 7:48 AM, Josh B <[EMAIL PROTECTED]> 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$gen, function(d) {
> d.clean <- d[,-1]
> cov(d.clean, y= NULL, use= "complete.obs", method= c("pearson")
> } )
>
> for more ideas, see ?by
>
> Cheers,
>
> Dylan
>
>
>
>
Works for me:
x <- read.csv('christina.txt')
x.list <- by(x, x$gen, function(d) {
d.clean <- d[,-1]
cov(d.clean, y= NULL, use= "complete.obs", method="pearson")
} )
note that the output is a list, where each element corresponds to one
level of 'gen'. if you need to write each element out to a file, see
?sapply or ?lapply .
Cheers,
Dylan
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