If you just want to permute columns of a matrix,
?sample
> sample.int(10)
[1] 9 2 10 8 4 6 3 1 5 7
and you can just use this as an index into the columns of your matrix,
presumably within a loop of some sort.
If I have misunderstood, just ignore.
Cheers,
Bert
On Tue, Feb 4, 2020 at 12:23 PM Ana Marija <sokovic.anamar...@gmail.com>
wrote:
> Hello,
>
> I have a matrix
> > dim(dat)
> [1] 15568 132
>
> It looks like this:
>
> NoD_14381_norm.1 NoD_14381_norm.2 NoD_14381_norm.3
> NoD_14520_30mM.1 NoD_14520_30mM.2 NoD_14520_30mM.3
> Ku8QhfS0n_hIOABXuE 4.75 4.25 4.79
> 4.33 4.63 3.85
> Bx496XsFXiAlj.Eaeo 6.15 6.23 6.55
> 6.26 6.24 5.99
> W38p0ogk.wIBVRXllY 7.13 7.35 7.55
> 7.37 7.36 7.55
> QIBkqIS9LR5DfTlTS8 6.27 6.73 6.45
> 5.39 4.75 4.96
> BZKiEvS0eQ305U0v34 6.35 7.02 6.76
> 5.45 5.25 5.02
> 6TheVd.HiE1UF3lX6g 5.53 5.02 5.36
> 5.61 5.66 5.37
>
> So it is a matrix with gene names ex. Ku8QhfS0n_hIOABXuE, and subjects
> named ex. NoD_14381_norm.1
>
>
> How to do 1000 permutations of these 132 columns and on each created
> new permuted matrix perform this code:
>
> subject="all_replicate"
> targets<-readTargets(paste(PhenotypeDir,"hg_sg_",subject,"_target.txt",
> sep=''))
> Treat <- factor(targets$Treatment,levels=c("C","T"))
> Replicates <- factor(targets$rep)
> design <- model.matrix(~Replicates+Treat)
> corfit <- duplicateCorrelation(dat, block = targets$Subject)
> corfit$consensus.correlation
> fit
> <-lmFit(dat,design,block=targets$Subject,correlation=corfit$consensus.correlation)
> fit<-eBayes(fit)
> qval.cutoff=0.1; FC.cutoff=0.17
> y1=topTable(fit, coef="TreatT",
> n=nrow(genes),adjust.method="BH",genelist=genes)
>
> y1 for each iteration of permutation would have P.Value column and
> these I would have plotted on the end to find the distribution of all
> p values generated in those 1000 permutations.
>
> Please advise,
> Ana
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
