Description Usage Arguments Value Author(s) Examples
Function to Sample Observations(gene expressions) from Independent Normal Distribution with Simulated sd
1 2 | sample.null.ind(ngenes.null.ind, n, sd.vector, var.ratio)
sample.alt.ind(ngenes.alt.ind, n, sd.vector, var.ratio, delta)
|
ngenes.null.ind |
an integer number for the number of observations (gene expression values) to simulate for genes coming from true null hypothesis |
n |
number of replicates for each group of control/treatment |
sd.vector |
vector of sd to sample from for controls |
var.ratio |
ratio of variance between treatment/control |
ngenes.alt.ind |
an integer number for the number of observations (gene expression values) to simulate for genes coming from true alternative hypothesis |
delta |
effect size, absolute difference of the means between genes from true alternative and true null nypothesis groups |
returns a matrix with ngenes.null.ind(or ngenes.alt.ind) rows and 2*n columns with the first n columns being samples from control group and last n columns being from treatment group for each gene (row)
Peng Liu peng\_liu@groton.pfizer.com
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | n.null.ind <- 50; n <- 500; var.ratio <- 1;
test.null.ind <- sample.null.ind(n.null.ind , n, var.ratio)
## Not run:
ndim <- dim(test.null.ind);
ssd.ctrl<-rep(0, ndim[1])
var.r <- rep(0, ndim[1])
k <- ceiling(n.null.ind * runif(1,0,1))
for ( i in c(1:ndim[1]))
{ssd.ctrl[i] <- sd(test.null.ind[i,1:n])
var.r[i] <- var(test.null.ind[i,(n+1):(2*n)]) / var(test.null.ind[i,1:n])}
cat("comparison between the desired sample and the generated sample: \n")
cat(" ------------------------------------------ \n",
"number of genes (rows) :\t", n.null.ind, "\t", ndim[1], "\n",
"number of obs for each group: \t", n, "\t", ndim[2]/2, "\n",
"variance ratio (trt/ctrl) is: \t", var.ratio, "\t", mean(var.r), "\n",
"variances for ctrl are generated randomly from inverse gamma distrn. \n",
"please check histogram of sd.\n",
"------------------------------------------ \n")
### Histogram of the standard deviations generated
hist(ssd.ctrl,n=20, col="cyan", border="blue", main="",
xlab="Standard Deviation (for simulated data)")
dens <- density(ssd.ctrl)
lines(dens$x, dens$y*par("usr")[4]/max(dens$y),col="red",lwd=2)
title("Histogram of Standard Deviations for generated sample")
## End(Not run)
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