[R] (no subject)
jim holtman
jholtman at gmail.com
Fri Oct 19 22:31:56 CEST 2007
You have this sequence of code in your script:
for (a in seq(1,(ncol(X)-3), by=2)){
for (b in seq(3,(ncol(X)-1), by=2)){
for (i in a){
j <- a+1
for (k in b){
l <- b+1
The 'for (i in a){' appears to meaningless since 'a' is just a single
value. What did you think this is supposed to do? Same for 'for (k
in b)'.
On 10/19/07, Luke Neraas <lukasneraas.r at gmail.com> wrote:
> # Hello
> # I have a question regarding pairwise calculations of a matrix using a
> "for-loop."
> # Below I have a matrix "X" with 8 columns. These are Genotypic data so
> Column1 & Column2 is
> # a unit, Column3 & Column4 is a unit, Column5 & Column6 is a unit, and
> Coulmn7 & 8 is a unit.
> # I have a loop designed to calculate the number of times an individual in
> Column"i" & Column"j"
> # has the same value and the same individual has two values that are the
> same in Column"k" & Column"l" .
> # I have another seires of code that adds a 2 in the poper location of a
> data frame called "result.df".
> # I have written a loop that accomplishes this "pair of columns" pairwise
> comparison, but it also compares
> # some of the "pairs of Columns" to themselves. Is there a way to get around
> this?
>
>
> # creation of the data matrix
> c1<- c(1,4,3,2,4,1,3,2,4,3)
> c2<- c(2,4,3,4,4,3,4,1,3,2)
> c3<- c(1,3,2,4,4,3,4,4,2,2)
> c4<- c(2,3,2,3,1,3,2,4,4,3)
> c5<- c(1,2,1,1,2,2,2,3,2,1)
> c6<- c(3,2,4,3,1,1,2,3,3,4)
> c7<- c(1,2,1,2,3,2,3,2,1,2)
> c8<- c(1,2,2,3,2,3,3,4,1,2)
>
> X<-cbind(c1,c2,c3,c4,c5,c6,c7,c8)
>
> X
>
> ## Creation of the result dataframe
> result<- matrix(0,16,2)
> result.df<-data.frame(result)
> result.df[,1] <- c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4)
> result.df[,2] <- c(1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4)
> names(result.df)[1]<-"L(A)a(i)"
> names(result.df)[2]<-"L(B)a(j)"
>
> result.df
>
>
>
> ### The loop written to find Double Homozygotes
>
>
> for (a in seq(1,(ncol(X)-3), by=2)){
> for (b in seq(3,(ncol(X)-1), by=2)){
> for (i in a){
> j <- a+1
> for (k in b){
> l <- b+1
>
> match.rows <- ((X [,i] == X [, j] ) & ( X [,k] == X [, l]))
>
> double_homo_i <- X [match.rows, i]
> double_homo_k <- X [match.rows, k]
>
> double_homo<- cbind( double_homo_i, double_homo_k)
> double_homo.df<-data.frame(double_homo,Counts=2)
> names(double_homo.df)[1]<-"L(A)a(i)"
> names(double_homo.df)[2]<- "L(B)a(j)"
>
>
> # Below takes each round throught he loop and puts in the result.dfdataframe.
>
> count<-double_homo.df
>
> almost.df<-aggregate(count$Counts, list(count[,1],count[,2]),
> FUN=sum)
>
> temp<-order(almost.df$Group.1)
> final.df<-almost.df[temp,]
> names(final.df)[1]<-"L(A)a(i)"
> names(final.df)[2]<-"L(B)a(j)"
>
> result.df<-merge(result.df,final.df,by=c("L(A)a(i)","L(B)a(j)"), all.x=T)
>
> }
> }
> }
> }
>
>
> # here is the result I get
>
> result.df
>
>
>
> # L(A)a(i) L(B)a(j) C1C2~C3C4 C1C2~C5C6 C1C2~C7C8 C3C4~C3C4 C3C4~C5C6
> C3C4~C7C8 C5C6~C3C4 C5C6~C5C6 C5C6~C7C8
> # 1 1 1 NA NA NA NA
> NA NA NA NA NA
> # 2 1 2 NA NA NA NA
> NA NA NA NA NA
> # 3 1 3 NA NA NA NA
> NA NA NA NA NA
> # 4 1 4 NA NA NA NA
> NA NA NA NA NA
> # 5 2 1 NA NA NA NA
> NA NA NA NA NA
> # 6 2 2 NA NA NA 2
> NA NA NA 4 2
> # 7 2 3 NA NA NA NA
> NA NA 2 NA 2
> # 8 2 4 NA NA NA NA
> NA NA NA NA NA
> # 9 3 1 NA NA NA NA
> NA NA NA NA NA
> # 10 3 2 2 NA NA NA
> 2 2 NA NA NA
> # 11 3 3 NA NA NA 4
> NA NA NA 2 NA
> # 12 3 4 NA NA NA NA
> NA NA 2 NA NA
> # 13 4 1 NA NA NA NA
> NA NA NA NA NA
> # 14 4 2 NA 2 2 NA
> NA NA NA NA NA
> # 15 4 3 2 NA NA NA
> 2 NA NA NA NA
> # 16 4 4 NA NA NA 2
> NA NA NA NA NA
>
>
>
>
>
> # Here is the Result I am looking for.
>
> L(A)a(i) L(B)a(j) C1C2~C3C4 C1C2~C5C6 C1C2~C7C8 C3C4~C5C6 C3C4~C7C8
> C5C6~C7C8
> # 1 1 1 NA NA NA NA
> NA NA
> # 2 1 2 NA NA NA NA
> NA NA
> # 3 1 3 NA NA NA NA
> NA NA
> # 4 1 4 NA NA NA NA
> NA NA
> # 5 2 1 NA NA NA NA
> NA NA
> # 6 2 2 NA NA NA NA
> NA 2
> # 7 2 3 NA NA NA NA
> NA 2
> # 8 2 4 NA NA NA NA
> NA NA
> # 9 3 1 NA NA NA NA
> NA NA
> # 10 3 2 2 NA NA 2
> 2 NA
> # 11 3 3 NA NA NA NA
> NA NA
> # 12 3 4 NA NA NA NA
> NA NA
> # 13 4 1 NA NA NA NA
> NA NA
> # 14 4 2 NA 2 2 NA
> NA NA
> # 15 4 3 2 NA NA 2
> NA NA
> # 16 4 4 NA NA NA NA
> NA NA
>
>
> # Any help or ideas 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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> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
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