R: Select observations according to IDR

select.IDR {idr} | R Documentation

## 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)

[Package idr version 1.2 Index]