Hello Rodrigo,
You're almost there:
you should make the variable distance before the while loop, and this should
be higher than 14 to go inside the while loop:
selectmarkers<- function(n=10){
tapply(mm$marker, mm$chr, function(m){
distances <- 15
while (max(distances) > 14) {
mars<- sort(sample(m, n))
distances<- rep(NA, (length(mars)-1))
for (i in 1:(length(mars)-1)) {
distances[i]<- mm[mars[i+1], 'loc'] - mm[mars[i], 'loc']
} #end of for loop
} # end of while loop
return (mars)
} # end of tapply f(m)
) #tapply
} # end of selectmarkers
Also take a look at the diff function, to get rid of the for loop:
selectmarkers2<- function(n=10){
tapply(mm$marker, mm$chr, function(m){
distances <-15
while (max(distances) > 14) {
mars<- sort(sample(m, n))
distances <- diff(mm[mars, 'loc'])
} # end of while loop
return (mars)
} # end of tapply f(m)
) #tapply
} # end of selectmarkers
for n = 10 this won't be a significant difference, but check for n=80:
system.time(selectmarkers(80)) #127 seconds at my system
system.time(selectmarkers2(80)) #1.44 seconds at my system
Kind regards
Bart Joosen
Rodrigo Gularte wrote:
>
> I am attempting to sample 10 markers from each chr, with a maximum
> distance
> of 14, calculated by the location of the marker in each chromosome as
> loc[i+1] - loc[i]. I presume the easiest way to do this is with a while
> loop, so that the function keeps resampling when the max distains is
> greater
> than 14. Example code is below.
>
> I have gon as far as to select markers and calculate the distances, A
> while
> loop with set with max(distances)>14 should work, but I'm not sure where
> to
> set this.
> Any help would be appreciated.
>
> Rodrigo
>
> #some markers, chromosomes and locations
> loc<- rep(1:100, 5)
> marker<- paste("A", seq(1:500), sep="")
> chr<- rep(1:5, rep(100,5))
> mm<- data.frame(marker, chr, loc)
>
> selectmarkers<-
> function(n=10){
> tapply(mm$marker, mm$chr, function(m){
>
> # while (max(distances) > 14) {
> mars<- sort(sample(m, n))
>
> distances<- rep(NA, (length(mars)-1))
>
> for (i in 1:(length(mars)-1)) {
> distances[i]<- mm[mars[i+1], 'loc'] - mm[mars[i], 'loc']
> } #end of for loop
> # } # end of while loop
>
> return (mars)
>
> } # end of tapply f(m)
> ) #tapply
> } # end of selectmarkers
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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