[R] sample

[Peter Ehlers]

On 2010-05-16 2:23, Laetitia Schmid wrote:
> Hi,
> I am sampling two random columns from females and two random columns
> from males to produce tetraploid offspring. For every female I am
> sampling a random male.
> In the end I want to write out a a matrix with all the offspring, but
> that does not work. I get always only the offspring from the last
> females. There must be a mistake in my script:
>
> moms<-read.delim("females.txt", stringsAsFactors=FALSE,header=TRUE)
> dads<-read.delim("males.txt", stringsAsFactors=FALSE,header=TRUE)
>
> output_offspring<-data.frame()
>
> for (i in 1:nrow(moms)){
> rdad=sample(1:nrow(dads),1)
> kid<-c(sample(moms[i,2:5],2),sample(dads[rdad,2:5],2))
> output_offspring<-rbind(output_offspring,c(moms$SampleID[i],dads$SampleID[rdad],kid))
>
> }

(When I run your code, I get an error.)

It's always best to pre-assign your output to have the
desired dimensions and then fill in the cells:

output_offspring <- as.data.frame(matrix("", nrow=nrow(moms), ncol=6), 
stringsAsFactors=FALSE)

for (i in 1:nrow(moms)){
    rdad <- sample(1:nrow(dads),1)
    kid <- c(sample(moms[i,2:5],2), sample(dads[rdad,2:5],2))
    output_offspring[i,] <- c(moms$SampleID[i], dads$SampleID[rdad], kid)
}

Personally, I would work with matrices, since all of your data
are string variables.

  -Peter Ehlers

> write.table(output_offspring,"offspring_7.txt",row.names=T,col.names=T,quote=F)
>
>
> females.txt:
>
> SampleID A1 A2 A3 A4
> GM920222 GATTGCC GATTGCC GATAGAC GATAGAC
> GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
> GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
> GM960023 GATTGCC GTCATCA GATTGCC GATTGCC
> GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
> GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
> GM920034 GATTGCC GTCATCA GATTGCA GATTGCA
> GM920096 GATTGCC GATTGCC GATTGCA GATTGCC
> GM930029 GTCATCA GATTGCC GTCATCA GATTGCC
> GM940031 GATTGCC GAGTGCA GATTGCA ACTAGAA
> GM960028 GATTGCC GAGTGCA GATTGCA ACTAGAA
> GM980007 GTCATCA GATTGCC ACTTGAA GTCATCA
> GM970009 ACTAGAA GTCAGAA GTCAGCA ACTAGCA
> GM930026 ACTAGAA GAGTGCA GAGTGCA ACTAGAA
> GM920031 GATTGCC GTCATCA GATTGCC GATTGCC
> GM990105 GATTGCC GATTGCC GTCAGCA GTCAGCA
> GM920202 GATTGCC GATTGCC GATTGCC GATTGCC
> GM920089 GAGTGCA GTCAGAA ACTATCA GATTGCC
> GM980051 ACTAGAA ACTAGAA GATAGCC GATAGCC
> GM930109 GTCATCA GAGTGCA GTTTTAA ACTAGAA
> GM940039 GTCATCA GAGTGCA GTTTGCC ACTTTCA
> GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
> GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
> GM030005 ACTAGAA GAGTGCA ACTAGAA ACTAGAA
> GM050009 ACTAGAA GATTGCC GATTGCC ACTAGAA
> GM990027 GATTGCC GAGTGCA GATTGCA GATTGCC
> GM990066 GATTGCC GTCATCA GTCATCA GATTGCC
>
> males.txt:
>
> SampleID A1 A2 A3 A4
> WI920425 ACTAGAA ACCATCA ACTAGAA ACTAGAA
> WI920408 ACTAGAA ACTAGAA ACTAGAA ACTAGAA
> WI920009 ACTAGAA ACTAGAA ACTAGAA GATTGCC
> WI920352 ACTTTCA ACGTTCA GAGAGAA GATTGCA
> WI920004 GATTGCC GATTGCC ACTAGAA ACTAGAA
> WI920353 ACTAGAA GATTGCC ACTAGAA GATTGCC
> WI920410 ACTAGAA GTCAGAA GAGTACC ACTTTCA
> WI920007 ACTAGAA ACTTTCA GAATGCA GTTAGAC
> WI920015 ACTTTCA ACGTTCA GTCAGAA GATTGCC
> WI920426 ACTAGAA GTCATCA GTCATCA ACTAGAA
> WI920433 ACTAGAA GTCAGAA GTCTGCA ACTTGCA
> WI920370 GATTGCC GAGTGCA GATTGCA ACTAGAA
> WI920437 GTCATCA GTCAGAA GATTGCC ACTTTCA
> WI920027 GATTGCC GAGTGCA GATTACC GATTGCC
> WI920415 GATTGCC GAGTGCA GTCATCA ACTAAAA
> WI920023 ACTTTCA GTCAGAA GAGATCA GATTGCC
> WI920360 GATTGCC GTCATCA GATTGCA ACTTTCA
> WI920017 GATTGCC GTCAGAA GATTTCC ACTAGCA
> WI920028 GTCATCA GTCAGAA GATTGCC ACTTGCA
> WI920361 GATTGCC GAGTGCA GTCAGCA GATTGCC
> WI920367 GATTGCC GATTGCC GTCATCA GATTGCC
> WI920366 GATTGCC GATTGCC GTCTGCA GTCTGCA
> WI920365 GATTGCC GAGTGCA GTCAGCA GTTTGCC
> WI920362 GATTGCC GAGTGCA GATTGCA ACTAGAA
> WI920441 GATTGCC GAGTGCA GATTGCA ACTAGAA
> WI920022 GTCATCA GTCAGAA GATTGCC ACTTTCA
> WI920356 GTCATCA GTCAGAA GATTGCC ACTTTCA
> WI920355 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920423 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920021 GATTGCC GATTGCC GTCAGCA GATTGCC
> WI920359 GATTGCC GATTGCC GTCAGCA GATTGCC
> WI920024 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920369 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920416 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920427 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920428 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920431 GATTGCC GATTGCC GATTGCC GATTGCC
> WI920001 GATTGCC GTCATCA GTCATCA GATTGCC
> WI920010 GATTGCC GTCATCA GTCATCA GATTGCC
> WI920349 GATTGCC GTCATCA GTCATCA GATTGCC
> WI920363 GATTGCC GTCATCA GTCATCA GATTGCC
> WI920417 GATTGCC GTCATCA GTCATCA GATTGCC
> WI920430 GATTGCC GTCATCA GTCATCA GATTGCC
>
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