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
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