estimate.m0: Estimate Number of True Null Hypotheses Using Histogram-based...

In rmRNAseq: RNA-Seq Analysis for Repeated-Measures Data

Description

This function estimates the number of true null hypotheses given a vector of p-values using the method of Nettleton et al. (2006) JABES 11, 337-356. The estimate obtained is identical to the estimate obtained by the iterative procedure described by Mosig et al. Genetics 157:1683-1698. The number of p-values falling into B equally sized bins are counted. The count of each bin is compared to the average of all the bin counts associated with the current bins and all bins to its right. Working from left to right, the first bin that has a count less than or equal to the average is identified. That average is multiplied by the total number of bins to obtain an estimate of m0, the number of tests for which the null hypothesis is true.

Usage

estimate.m0(p, B = 20)

Arguments

p	a numerical vector of p-value
B	number of bin

Value

The function returns an estimate of m0, the number of tests for which the null hypothesis is true.

Author(s)

Dan Nettleton [e-mail]

References

1. Dan Nettleton, J. T. Gene Hwang, Rico A. Caldo and Roger P. Wise. Estimating the Number of True Null Hypotheses from a Histogram of p Values. Journal of Agricultural, Biological, and Environmental Statistics Vol. 11, No. 3 (Sep., 2006), pp. 337-356.

Examples

data(res)
p <- res$pqvalue$pv$line2
m0 <- rmRNAseq:::estimate.m0(p)
m0

rmRNAseq documentation built on Nov. 8, 2019, 5:06 p.m.