Qvalue: Storey's (2001) q-value Procedure...

In mutoss: Unified Multiple Testing Procedures

Storey's (2001) q-value Procedure...

Description

Storey's (2001) q-value Procedure

Usage

Qvalue(pValues, lambda=seq(0, 0.9, 0.05), pi0.method="smoother",
    fdr.level=NULL, robust=FALSE, smooth.df=3, smooth.log.pi0=FALSE,
    silent=FALSE)

Arguments

pValues	pValues to be used (only necessary input)
lambda	Value of the tuning parameter to be used
pi0.method	Method for automatically choosing tuning parameter in the estimation of pi_0. Either 'smoother' or 'bootstrap'
fdr.level	Level at which to control the FDR
robust	Logical, whether to make estimate more robust for small p-values.
smooth.df	Number of degrees of freedom to use when estimating pi_0 with the smoother.
smooth.log.pi0	Logical, if TRUE and pi0.method = 'smoother', pi0 will be estimated by applying a smoother to a scatterplot of log(pi_0) estimates against the tuning parameter lambda.
silent	logical scalar. If TRUE no output is generated.

Details

The Qvalue procedure estimates the q-values for a given set of p-values. The q-value of a test measures the proportion of false positive incurred when that particular test is called sigificant. It gives the scientist a hypothesis testing error measure for each observed statistic with respect to the pFDR.

Note: If no options are selected, then the method used to estimate pi0 is the smoother method desribed in Storey and Tibshirani (2003). The bootstrap method is described in Storey, Taylor and Siegmund (2004).

Value

A list containing:

qValues	A vector of the estimated q-values
pi0	An estimate of the proportion of null hypotheses
errorControl	A Mutoss S4 class of type errorControl, containing the type of error controlled by the function.

Author(s)

HackNiklas

References

Storey, John (2001). The Positive False Discovery Rate: A Baysian Interpretation and the Q-Value. The Annals of Statistics, Vol. 31, No. 6, 2013-2035.

Examples

pval <- c(runif(50), runif(50, 0, 0.01))
result <- Qvalue(pval)
result <- Qvalue(pval, lambda=0.5)

mutoss documentation built on March 31, 2023, 8:46 p.m.