empPvalues: Estimate empirical p-values for Chi^2 protein correlations.
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Usage Arguments Value Author(s) References See Also Examples

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.

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

`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`.

A numeric of length nrow(corMatrix).

Laurent Gatto <lg390@cam.ac.uk>

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.

chi2 for Chi^2 calculation.

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)