[R] Trouble obtaining results from a loop

[jim holtman]

I think this gives you what you are looking for:

> P.genotype.sample
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    2    6    2    2    3    6    1    5    5     5
 [2,]    2    3    2    8    3    3    5    5    5     8
 [3,]    1    3    2    8    8    8    5    5    8     8
 [4,]    5    6    3    3    3    8    1    5    5     8
 [5,]    1    8    3    8    6    6    5    7    5     8
 [6,]    1    1    2    2    1    8    1    6    5     5
 [7,]    5    6    2    8    1    7    1    7    5     8
 [8,]    6    7    2    3    1    3    5    5    2     5
 [9,]    1    2    3    4    1    1    5    5    5     8
[10,]    3    3    3    3    3    7    5    8    2     2
>
> # create result matrix
> result <- matrix(0, ncol=5, nrow=8)
>
> # iterate for pairs of columns
> for (i in seq(1, ncol(P.genotype.sample), by=2)){
+     # get the rows that match
+     match.row <- P.genotype.sample[,i] == P.genotype.sample[, i + 1]
+     # get the values from the rows that match
+     same <- P.genotype.sample[match.row, i]
+     # now increment the 'result' matrix
+     for (j in same) result[j, (i + 1) / 2] <- result[j, (i + 1) / 2] + 1
+ }
> result
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    0    1    0    0
[2,]    0    2    0    0    1
[3,]    1    2    1    0    0
[4,]    0    0    0    0    0
[5,]    0    0    0    4    2
[6,]    0    0    1    0    0
[7,]    0    0    0    0    0
[8,]    0    0    1    0    1
>


On 10/2/07, Luke Neraas <lukasneraas.r at gmail.com> wrote:
> #Hello,
> #I have a question about obtaining results from a loop I have written.
> #Below is a sample of individual genotypes from a genetic question I am
> working on called "P.genotype.sample ".
>
> P.genotype.sample<-matrix(10,10,10)
> P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3)
> P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3)
> P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)
> P.genotype.sample[,4]<-c(2,8,8,3,8,2,8,3,4,3)
> P.genotype.sample[,5]<-c(3,3,8,3,6,1,1,1,1,3)
> P.genotype.sample[,6]<-c(6,3,8,8,6,8,7,3,1,7)
> P.genotype.sample[,7]<-c(1,5,5,1,5,1,1,5,5,5)
> P.genotype.sample[,8]<-c(5,5,5,5,7,6,7,5,5,8)
> P.genotype.sample[,9]<-c(5,5,8,5,5,5,5,2,5,2)
> P.genotype.sample[,10]<-c(5,8,8,8,8,5,8,5,8,2)
> P.genotype.sample
>
> # I would like to count the number of times the same number ( 1 through 8)
> occurs in each row
> # and only in pairs of columns; 1:2, 3:4, 5:6, 7:8, & 9:10.  below is the
> loop that i have written
> # to perform this operation and put in the results in a matrix that is 5
> columns wide and 8 rows long (called "result").
> # I can get the operation to run but it gives me the results for the last
> pair of columns and overwrites
> # the results into every column of my result matrix. I am puzzled as to why
> this is occurring.
>
> Loci<-5
> Locus.Columns<- Loci*2
>
> x<-seq(1,Locus.Columns,2)
>
> result<-matrix(8,8,Loci)
>
>
> for (i in 1:Loci){
>    for (j in 1:8){
>        for (k in x){
>    result[j,i] <- sum(P.genotype.sample[,k]==j & P.genotype.sample[,k+1]==j)
>
>        }
>        }
>        }
>
> result
>
>
> # Below is a long and drawn out way to achieve the result I am looking for
> in the loop above.
>
> true.result<-matrix(8,8,Loci)
>
>    for(j in 1:8){
> true.result[j,1] <-sum(P.genotype.sample[,1]==j & P.genotype.sample[,2]==j)
>        }
>
>    for(j in 1:8){
> true.result[j,2] <-sum(P.genotype.sample[,3]==j & P.genotype.sample[,4]==j)
>        }
>
>    for(j in 1:8){
> true.result[j,3] <-sum(P.genotype.sample[,5]==j & P.genotype.sample[,6]==j)
>        }
>
>    for(j in 1:8){
> true.result[j,4] <-sum(P.genotype.sample[,7]==j & P.genotype.sample[,8]==j)
>        }
>
>    for(j in 1:8){
> true.result[j,5] <-sum(P.genotype.sample[,9]==j & P.genotype.sample[,10]==j)
>        }
>
> true.result
>
> # Any suggestions or help on how to make this loop work would be greatly
> appreciated.
>
> # Thanks in advance
>
>
> Luke Neraas
>
> lukasneraas.r at gmail.com
>
> University of Alaska Fairbanks
> School of Fisheries and Ocean Sciences
> 11120 Glacier Highway
> UAF Fisheries Division
> Juneau, AK 99801
>
>        [[alternative HTML version deleted]]
>
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>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?