p2SNR {PANR} | R Documentation |
The function translate p-values to Signal-to-Noise Ratios based on the fitted mixture model.
p2SNR(object, pval, ...)
object |
an object of S4 class |
pval |
a numeric or integer specifying the p-value to translate |
... |
not in use, only for further extension. |
The function will return a data frame including p-values, lower and upper quantiles and corresponding Signal-to-Noise Ratios.
Xin Wang xw264@cam.ac.uk
Xin Wang, Mauro Castro, Klaas W. Mulder and Florian Markowetz, Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, in preparation.
## Not run: data(Bakal2007) bm1<-new("BetaMixture", pheno=Bakal2007, model="global", order=1) bm1<-fitNULL(bm1, nPerm=10, thetaNULL=c(alphaNULL=4, betaNULL=4), sumMethod="median", permMethod="all", verbose=TRUE) bm1<-fitBM(bm1, para=list(zInit=NULL, thetaInit=c(alphaNeg=2, betaNeg=4, alphaNULL=bm1@result$fitNULL$thetaNULL[["alphaNULL"]], betaNULL=bm1@result$fitNULL$thetaNULL[["betaNULL"]], alphaPos=4, betaPos=2), gamma=NULL), ctrl=list(fitNULL=FALSE, tol=1e-1), verbose=TRUE, gradtol=1e-3) p2SNR(bm1, pval=0.01) ## End(Not run)