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
Laurent Gatto <lg390@cam.ac.uk>
See also
chi2 for \(Chi^2\) calculation.
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.
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)
#> [1] 0.92 0.43 0.62 0.23 0.49 0.49 0.42 0.19 0.85 0.59 0.83 0.44 0.78 0.83 0.92
#> [16] 0.90 0.34 0.62 0.18 0.32 0.00