[R] doing 1000 permutations and doing test statistics distribution

[Bert Gunter]

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.anamarija using 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
>
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