select.IDR: Select observations according to IDR

In idr: Irreproducible Discovery Rate

Select observations according to IDR

Description

Select observations that exceeding a given IDR level

Usage

select.IDR(x, IDR.x, IDR.level)

Arguments

x	a n by m numeric matrix, where m= num of replicates, n=num of observations. Numerical values representing the significance of the observations, where larger values represent higher significance, for example, -log(p-value). Currently, m=2.
IDR.x	Irreproducibile discovery rate for each entry of x. It is computed from est.IDR().
IDR.level	IDR cutoff, a numerical value between [0,1].

Value

x	Observations that are selected.
n	Number of observations that are selected.
IDR.level	IDR cutoff, a numerical value between [0,1].

Author(s)

Qunhua Li

References

Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.

See Also

est.IDR

Examples

data("simu.idr")
x <- cbind(-simu.idr$x, -simu.idr$y)

mu <- 2.6
sigma <- 1.3
rho <- 0.8
p <- 0.7

idr.out <- est.IDR(x, mu, sigma, rho, p, eps=0.001, max.ite=20)
# select observations exceeding IDR threshold=0.01 
IDR.level <- 0.01
x.selected <- select.IDR(x, idr.out$IDR, IDR.level)

idr documentation built on June 21, 2022, 9:05 a.m.