R help - Jul 2011 - Avoiding loops to detect number of coincidences

Hi all,

I have this information on a file ht.txt, imagine it is a data frame without
labels:

1 1 1 8 1 1 6 4 1 3 1 3 3
And on other table called "pru.txt" I have sequences similar this

4 1 1 8 1 1 6 4 1 3 1 3 3
1 6 1 8 1 1 6 4 1 3 1 3 3
1 1 1 8 1 1 6 4 1 3 1 3 3
6 6 6 8 1 1 6 4 1 3 1 3 3
I want to now how many positions are identical between each row
in pru compared with ht.

n and m are the col and row of pru (m is the same number in pru and ht)

I tried this with loops

n<-nrow(pru)
m<-ncol(pru)

dacc2<-mat.or.vec(n, m)

for (g in 1:n){
for (j in 1:m){
if(pru[g,j]-ht[1,j]!=0) dacc2[g,j]=0 else {dacc2[g,j]=1}
}
}

So when I have dacc2 I can filter this:

dar2<-pru[colSums(dacc2)>2 & colSums(dacc2)<10,]

There is some way to avoid loops?

	[[alternative HTML version deleted]]

Hi Trying,

It would be helpful if you provided reproducible examples. It would
also be polite to sign a name so that we have something by which to
address you.

On Tue, Jul 12, 2011 at 8:00 AM, Trying To learn again
<tryingtolearnagain at gmail.com> wrote:
> Hi all,
>
> I have this information on a file ht.txt, imagine it is a data frame
without
> labels:
>
> 1 1 1 8 1 1 6 4 1 3 1 3 3
> And on other table called "pru.txt" I have sequences similar this
>
> 4 1 1 8 1 1 6 4 1 3 1 3 3
> 1 6 1 8 1 1 6 4 1 3 1 3 3
> 1 1 1 8 1 1 6 4 1 3 1 3 3
> 6 6 6 8 1 1 6 4 1 3 1 3 3
> I want to now how many positions are identical between each row
> in pru compared with ht.
I have no idea what you are trying to do with the loops below, but if
you are trying to count matches by row:
> a reproducible example
> dput(ht)
c(1, 1, 1, 8, 1, 1, 6, 4, 1, 3, 1, 3, 3)
> dput(pru)
structure(list(V1 = c(4L, 1L, 1L, 6L), V2 = c(1L, 6L, 1L, 6L),
    V3 = c(1L, 1L, 1L, 6L), V4 = c(8L, 8L, 8L, 8L), V5 = c(1L,
    1L, 1L, 1L), V6 = c(1L, 1L, 1L, 1L), V7 = c(6L, 6L, 6L, 6L
    ), V8 = c(4L, 4L, 4L, 4L), V9 = c(1L, 1L, 1L, 1L), V10 = c(3L,
    3L, 3L, 3L), V11 = c(1L, 1L, 1L, 1L), V12 = c(3L, 3L, 3L,
    3L), V13 = c(3L, 3L, 3L, 3L)), .Names = c("V1", "V2",
"V3",
"V4", "V5", "V6", "V7", "V8",
"V9", "V10", "V11", "V12",
"V13"
), class = "data.frame", row.names = c(NA,
-4L))
> # count the positional matches by row
> apply(pru, 1, function(x)sum(x == ht))
[1] 12 12 13 10

Sarah

> n and m are the col and row of pru (m is the same number in pru and ht)
>
> I tried this with loops
>
> n<-nrow(pru)
> m<-ncol(pru)
>
> dacc2<-mat.or.vec(n, m)
>
> for (g in 1:n){
> for (j in 1:m){
> if(pru[g,j]-ht[1,j]!=0) dacc2[g,j]=0 else {dacc2[g,j]=1}
> }
> }
>
> So when I have dacc2 I can filter this:
>
> dar2<-pru[colSums(dacc2)>2 & colSums(dacc2)<10,]
>
> There is some way to avoid loops?
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Sarah Goslee
http://www.functionaldiversity.org