PsiHat (version 1.0)

p0est: Estimates the proportion of unaffected features (p0).

Description

Estimates the proportion of null hypothesis (unaffected features) (p0). It is a wrapper of function qvalue from R package qvalue.

Usage

p0est(pvalue, lambda = seq(0, 0.9, 0.05), pi0.method = "smoother", smooth.df = 3, smooth.log.pi0 = FALSE, fdr.level = NULL)

Arguments

pvalue

Vector of p-values.

lambda

Tuning parameter in [0,1) to estimate p0.

pi0.method

Method to estimate the proportion of true null hypothesis (p0): "smoother" or "bootstrap".

smooth.df

If pi0.method="smoother", number of degrees-of-freedom.

smooth.log.pi0

If pi0.method="smoother" and smooth.log.pi0=TRUE, p0 is estimated by applying a smoother to log p0 estimates against the tuning parameter lambda.

fdr.level

A level at which to control the FDR. Must be in (0,1]

Value

See Also

qvalue package, lfdr.bbe and nqvalue.

Examples

# a p-value with missing elements:
y <- runif(15) ;y[c(13, 2,5)] <- NA
z1 <- p0est(pvalue = y, lambda = 0.5)
z2 <- p0est(pvalue = y, pi0.method = "bootstrap")