empPvalues {pRoloc} | R Documentation

## Estimate empirical p-values for Chi^2 protein correlations.

### Description

Andersen et al. (2003) used a fixed Chi^2 threshold of 0.05 to identify organelle-specific candidates. This function computes empirical p-values by permutation the markers relative intensities and computed null Chi^2 values.

### Usage

    empPvalues(marker, corMatrix, n = 100, ...)

### Arguments

`marker` | A `numerics` with markers relative intensities.
`corMatrix` | A `matrix` of `nrow(corMatrix)` protein relative intensities to be compares against the marker.
`n` | The number of iterations.
`...` | Additional parameters to be passed to `chi2`.

### Value

A `numeric` of length `nrow(corMatrix)`.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### References

Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P. et al., Proteomic characterization of the human centrosome by protein correlation profiling. Nature 2003, 426, 570 - 574.

### See Also

`chi2` for Chi^2 calculation.

### Examples

    set.seed(1)
    mrk <- rnorm(6, 5, 1)
    prot <- rbind(matrix(rnorm(120, 5, 1), ncol = 6),
                  mrk + rnorm(6))
    mrk <- mrk/sum(mrk)
    prot <- prot/rowSums(prot)
    empPvalues(mrk, prot)

[Package pRoloc version 1.30.0 Index]